Protein binding miniature proteins

ABSTRACT

The present invention provides a protein scaffold, such as an avian pancreatic polypeptide, that can be modified by substitution of two or more amino acid residues that are exposed on the alpha helix domain of the polypeptide when the polypeptide is in a tertiary form.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.10/982,727, filed Nov., 4, 2004, which is a continuation-in-part of U.S.patent application Ser. No. 09/840,085 filed Apr. 24, 2001, which claimsthe benefit of U.S. Provisional Application No. 60/199,408 filed Apr.24, 2000; No. 60/240,566 filed Oct. 16, 2000; and U.S. ProvisionalApplication No. 60/265,099 filed Jan. 30, 2001; and No. 60/271,368 filedFeb. 23, 2001. 10/982,727 also claims priority to U.S. ProvisionalPatent Application No. 60/517,496 filed on Nov. 4, 2003. The teachingsof these referenced applications are incorporated herein by reference intheir entirety.

FUNDING

Work described herein was funded, in whole or in part, by NationalInstitutes of Health, Grant Numbers 5-R01-GM59483 and 1-R01-GM65453-01.The United States government has certain rights in the invention.

FIELD OF THE INVENTION

The present invention relates to a polypeptide scaffold, such as anavian pancreatic polypeptide, that is modified by substitution of atleast one amino acid residue that is exposed on the alpha helix domainof the polypeptide when the polypeptide is in a tertiary form. Theinvention also relates to phage display libraries for such scaffolds.

BACKGROUND OF THE INVENTION

Many proteins recognize nucleic acids, other proteins or macromolecularassemblies using a partially exposed alpha helix. Within the context ofa native protein fold, such alpha helices are usually stabilized byextensive tertiary interactions with residues that may be distant inprimary sequence from both the alpha helix and from eachother. Withnotable exceptions (Armstrong et al., (1993) J. Mol. Biol. 230,284-291), removal of these tertiary interactions destabilizes the alphahelix and results in molecules that neither fold nor function inmacromolecular recognition (Zondlo & Schepartz, (1999) J. Am. Chem. Soc.121, 6938-6939). The ability to recapitulate or perhaps even improve onthe recognition properties of an alpha helix within the context of asmall molecule should find utility in the design of synthetic mimeticsor inhibitors of protein function (Cunningham et al., (1997) Curr. Opin.Struct. Biol. 7, 457-462) or new tools for proteomics research.

Two fundamentally different approaches have been taken to bestow alphahelical structure on otherwise unstructured peptide sequences. Oneapproach makes use of modified amino acids or surrogates that favorhelix initiation (Kemp et al., (1991) J. Org. Chem. 56, 6683-6697) orhelix propagation (Andrews & Tabor, (1999) Tetrahedron 55, 11711-11743;Blackwell & Grubbs, (1998) Angew. Chem. Int. Ed. Eng. 37, 3281-3284;Schafmeister et al., (2000) J. Am. Chem. Soc. 122, 5891-5892). Perhapsthe greatest success has been realized by joining the i and i+7positions of a peptide with a long-range disulfide bond to generatemolecules whose helical structure was retained at higher temperatures(Jackson et al., (1991) J. Am. Chem. Soc. 113, 9391-9392). A secondapproach (Cunningham et al., (1997) Curr. Opin. Struct. Biol. 7,457-462; Nygren, (1997) Curr. Opin. Struct. Biol. 7, 463-469), is topare the extensive tertiary structure surrounding a given recognitionsequence to generate the smallest possible molecule possessing function.This strategy has generated minimized versions of the Z domain ofprotein A (fifty-nine amino acids) and atrial natriuretic peptide(twenty-eight amino acids). The two minimized proteins, at thirty-threeand fifteen amino acids, respectively, displayed high biologicalactivity (Braisted & Wells, (1996) Proc. Natl. Acad. Sci., USA 93,5688-5692; Li et al., (1995) Science 270, 1657-1660). Despite thissuccess, it is difficult to envision a simple and general application ofthis truncation strategy in the large number of cases where the alphahelical epitope is stabilized by residues scattered throughout theprimary sequence.

In light of this limitation, a more flexible approach to proteinminimization called protein grafting has been employed. Schematically,protein grafting involves removing residues required for molecularrecognition from their native alpha helical context and grafting them onthe scaffold provided by small yet stable proteins. Numerous researchershave engineered protein scaffolds to present binding residues on arelatively small peptide carrier. These scaffolds are small polypeptidesonto which residues critical for binding to a selected target can begrafted. The grafted residues are arranged in particular positions suchthat the spatial arrangement of these residues mimics that which isfound in the native protein. These scaffolding systems are commonlyreferred to as miniproteins. A common feature is that the bindingresidues are known before the miniprotein is constructed.

Examples of these miniproteins include the thirty-seven amino acidprotein charybdotoxin (Vita et al., (1995) Proc. Natl. Acad. Sci. USA92, 6404-6408; Vita et al., (1998) Biopolymers 47, 93-100) and thethirty-six amino acid protein, avian pancreatic peptide (Zondlo &Schepartz, (1999) Am. Chem. Soc. 121, 6938-6939). Avian pancreaticpolypeptide (aPP) is a polypeptide in which residues fourteen throughthirty-two form an alpha helix stabilized by hydrophobic contacts withan N-terminal type II polyproline (PPII) helix formed by residues onethrough eight. Because of its small size and stability, aPP is anexcellent scaffold for protein grafting of alpha helical recognitionepitopes (Zondlo & Schepartz, (1999) J. Am. Chem. Soc. 121, 6938-6939).

SUMMARY OF THE INVENTION

The invention encompasses an avian pancreatic polypeptide modified bysubstitution of at least one amino acid residue; this residue is exposedon the alpha helix domain of the polypeptide when the polypeptide is ina tertiary form. In some embodiments, the modified polypeptide containsat least six substituted residues, while in other embodiments itcontains eight substituted residues, while in another embodiment itcontains ten substituted residues, while in yet another embodiment itcontains at least twelve substituted residues.

The substituted residues are selected from a site on a known proteinthrough which interaction with another molecule occurs. For example, oneor more amino acid residues present in (of) a site on a known proteinthrough which the known protein interacts (e.g., binds) with a bindingpartner replace one or more amino acid residues of the avian pancreaticpolypeptide. Known proteins include, but are not limited to, GCN4, CEBP,Max, Myc, MyoD, double minute two, Bcl-2, protein kinase A, Jun and Fos.In a preferred embodiment, the site on the known protein is a bindingsite. In some embodiments the modified avian pancreatic polypeptide iscapable of inhibiting the interaction between the known protein andanother molecule while in other embodiments it is capable of enhancingthe interaction. In some embodiments, the binding site is a DNA bindingsite while in others it is a protein binding site. Preferred DNA bindingsites include, but are not limited to the CRE half site, the CEBP site,the MyoD half site and the Q50 engrailed variant site.

The invention also encompasses a phage-display library comprising aplurality of recombinant phage that express any of the aforementionedmodified avian pancreatic polypeptides of the invention. In a relatedembodiment, the invention encompasses a phage-display library comprisinga plurality of recombinant phage that express a protein scaffoldmodified by substitution of at least one amino acid residue, thisresidue being exposed on the polypeptide when the polypeptide is in atertiary form. In some embodiments, the protein scaffold of thephage-display library comprises the avian pancreatic polypeptide. Theinvention also encompasses an isolated phage selected from the phagelibrary of the invention.

In specific embodiments, the invention is a modified avian pancreaticpolypeptide (aPP) comprising substitution of at least one amino acidresidue, said at least one residue being exposed on the alpha helixdomain of the polypeptide when the polypeptide is in a tertiary form,wherein the modified polypeptide binds to a target protein. In specificembodiments, at least six amino acid residues, at least eight amino acidresidues, at lease ten amino acid residues or at least twelve amino acidresidues are substituted. In certain embodiments, the site is aprotein-binding site. The at least one substituted residues can be fromany site of a known protein through which the known protein interactswith its binding partner. The target protein can be, for example, abinding partner of the known protein, which can be, for example, a Bcl2protein, p53, a protein kinase inhibitor (PKI), or CREB. The bindingpartner can be, for example, selected from the group consisting of aBcl2 protein, MDM2, protein kinase A or CBP. A variety of modifiedpolypeptides can be produced, such as a modified polypeptide thatinhibits interaction between the known protein and the binding partner;a modified polypeptide that binds to a deep groove of the targetprotein; a modified polypeptide that binds to the groove of the targetprotein, wherein the groove is more than 6 Å at deepest point; amodified polypeptide that binds to a shallow groove of the targetprotein; a modified polypeptide that binds to the shallow groove of thetarget protein, wherein the groove is less than 6 Å at deepest point.The modified polypeptide can bind to the target protein with a Kd ofless than 1 micromolar or to the target protein with high specificity.

In certain embodiments, the modified polypeptide comprises an amino acidsequence selected from the sequence represented in FIGS. 1, 2, 6, 8 orTable 1.

Further embodiments of the invention are as follows, with reference tothe appended claims:

19. A stabilized miniature protein comprising a miniature protein and asecond portion comprising a stabilizing domain, wherein the miniatureprotein is a modified avian pancreatic polypeptide (aPP) comprisingsubstitution of at least one amino acid residue, said at least oneresidue being exposed on the alpha helix domain of the polypeptide whenthe polypeptide is in a tertiary form, wherein the modified polypeptidebinds to a target protein.

20. The stabilized miniature protein of claim 19, wherein the secondportion is a polypeptide covalently fused to the miniature protein.

21. The stabilized miniature protein of claim 20, wherein the secondportion is selected from the group consisting of serum albumin and anIgG Fc domain.

22. The stabilized miniature protein of claim 19, wherein the secondportion is a non-amino acid moiety.

23. The stabilized miniature protein of claim 19, wherein said miniatureprotein includes one or more modified amino acid residues selected fromthe group consisting of a phosphorylated amino acid, a glycosylatedamino acid, a PEGylated amino acid, a farnesylated amino acid, anacetylated amino acid, a biotinylated amino acid, an amino acidconjugated to a lipid moiety, and an amino acid conjugated to an organicderivatizing agent.

24. A pharmaceutical preparation comprising: a) a modified polypeptideof claim 1; and b) a pharmaceutically acceptable carrier.

25. The pharmaceutical preparation of claim 24, wherein said preparationis substantially pyrogen free.

26. A pharmaceutical preparation comprising: a) a stabilized miniatureprotein of claim 19; and b) a pharmaceutically acceptable carrier.

27. The pharmaceutical preparation of claim 26, wherein said preparationis substantially pyrogen free.

28. A phage-display library comprising a plurality of recombinant phagethat express the modified avian pancreatic polypeptide of claim 1.

29. A phage-display library comprising a plurality of recombinant phagethat express a protein scaffold modified by substitution of at least oneamino acid residue, said at least one residue being exposed on thepolypeptide when the polypeptide is in a tertiary form, wherein themodified polypeptide binds to a target protein.

30. The phage-display library of claim 29, wherein said protein scaffoldcomprises an avian pancreatic polypeptide (aPP).

31. A phage selected from the library of claim 29.

32. An isolated avian pancreatic polypeptide modified by substitution ofat least one amino acid residue, wherein the modified polypeptidecomprises a sequence selected from the group consisting of:

(a) an amino acid sequence selected from FIGS. 1, 2, 6, 8, and Table 1;(b) a fragment of at least twelve (12) amino acids of any amino acidsequence selected from FIGS. 1, 2, 6, 8, and Table 1;(c) an amino acid sequence selected from FIGS. 1, 2, 6, 8, and Table 1;comprising one or more conservative amino acid substitutions;(d) an amino acid sequence selected from FIGS. 1, 2, 6, 8, and Table 1;comprising one or more naturally occurring amino acid sequencesubstitutions; and(e) an amino acid sequence at least 95% identical to any amino acidsequence selected from FIGS. 1, 2, 6, 8, and Table 1.

33. An isolated nucleic acid encoding any one of the polypeptides inclaim 32.

34. A recombinant polynucleotide comprising a promoter sequence operablylinked to a nucleic acid of claim 33.

35. A cell transformed with a recombinant polynucleotide of claim 34.

36. The cell of claim 35, wherein the cell is a mammalian cell.

37. The cell of claim 35, wherein the cell is a human cell.

38. A method of making a miniature protein, comprising:

a) culturing a cell under conditions suitable for expression of theminiature protein, wherein said cell is transformed with a recombinantpolynucleotide of claim 34; andb) recovering the miniature protein so expressed.

39. A method of preparing a miniature protein that modulates theinteraction between a known protein and another molecule, comprising thesteps of:

(a) identifying at least one amino acid residue that contributes to thebinding between a known protein and another molecule; and(b) modifying an avian pancreatic polypeptide by substitution of said atleast one amino acid residue, such that it is exposed on the alpha helixdomain of the polypeptide when the polypeptide is in a tertiary form.

40. A method of identifying a miniature protein that modulates theinteraction between a known protein and another molecule, comprisingisolating at least one recombinant phage clone from the phage displaylibrary of claim 29 that displays a protein scaffold that modulates theassociation between a known protein and another molecule.

41. A method for treating a subject having a disorder associated withabnormal cell growth and differentiation, comprising administering tothe subject an effective amount of a miniature protein.

42. The method of claim 41, wherein the disorder is selected from thegroup consisting of inflammation, allergy, autoimmune diseases,infectious diseases, and tumors.

43. The method of claim 41, wherein the miniature protein is selectedfrom the group consisting of:

a) a modified polypeptide of claim 1;b) a stabilized miniature protein of claim 19; andc) an modified avian pancreatic polypeptide of claim 32.

44. A method of activating p53 function in a cell, comprising contactingthe cell with a miniature protein or a stabilized miniature protein.

45. The method of claim 44, wherein the miniature protein or stabilizedminiature protein comprises an amino acid sequence selected from FIG. 2.

46. The method of claim 44, wherein the miniature protein or stabilizedminiature protein inhibits binding of p53 to MDM2.

47. The method of claim 44, wherein the cell is a mammalian cell.

48. The method of claim 44, wherein the cell is a cancer cell.

49. A method of inhibiting a protein kinase activity in a cell,comprising contacting the cell with a miniature protein or a stabilizedminiature protein.

50. The method of claim 49, wherein the miniature protein or stabilizedminiature protein comprises an amino acid sequence selected from FIG. 6.

51. The method of claim 49, wherein the miniature protein or stabilizedminiature protein binds to the protein kinase.

52. The method of claim 49, wherein the protein kinase is PKA.

53. The method of claim 49, wherein the miniature protein or stabilizedminiature protein is conjugated with a protein kinase inhibitor (PKI).

54. The method of claim 49, wherein the cell is a mammalian cell.

55. The method of claim 49, wherein the cell is a cancer cell.

56. A method of activating CBP function in a cell, comprising contactingthe cell with a miniature protein or a stabilized miniature protein.

57. The method of claim 56, wherein the miniature protein or stabilizedminiature protein comprises an amino acid sequence selected from FIG. 8and Table 1.

58. The method of claim 56, wherein the miniature protein or stabilizedminiature protein binds to CBP.

59. The method of claim 56, wherein the miniature protein or stabilizedminiature protein activates transcription via a CBP-dependent pathway.

60. The method of claim 56, wherein the cell is a mammalian cell.

61. The method of claim 56, wherein the cell is a cancer cell.

62. Use of a miniature protein or stabilized miniature protein formaking a medicament for the treatment of a disorder associated withabnormal cell growth and differentiation.

63. The method of claim 62, wherein the disorder is selected from thegroup consisting of inflammation, allergy, autoimmune diseases,infectious diseases, and tumors.

BRIEF DESCRIPTION OF THE DRAWINGS

The file of this patent contains at least one drawing executed in color.Copies of this patent with color drawing(s) will be provided by thePatent and Trademark Office upon request and payment of the necessaryfee.

FIG. 1—Seven distinct sequences isolated from BAKLIB phage library.Dissociation constants for miniature protein binding to Bcl-2 are shownon the right.

FIGS. 2A-B—(A) Protein grafting as applied to the design of miniatureprotein ligands for MDM2. (B) Sequence alignment of aPP and p53AD.Residues in yellow and blue stabilize the aPP hydrophobic core; those inred contribute to the binding of MDM2. Residues varied in Library #1 arein purple. Each K_(d) reported represents the equilibrium dissociationconstant of the peptide·GST-MDM2 complex determined by fluorescencepolarization analysis. GST-MDM2 was over-expressed in BL21 cells usingclone G.

FIG. 3—Fluorescence polarization analysis of the affinity of GST-MDM2for selected peptides and the affinity of pP53-05 for selected proteins.Plots illustrate the fraction of fluorescein-labeled p53AD, pP53-05,pP53-03, pP53-04, pP53-01, pP53-02 bound as a function of GST-MDM2concentration; and the fraction of fluorescein-labeled pP53-05 bound (Θ)as a function of (⋄) protein kinase A, (Δ) Fos, (∘) carbonic anhydrase,(□) calmodulin. Each point represents the average of at least threetrials. Error bars represent the standard error. K_(d) values werecalculated as described in Heyduk, et al., Proc Natl Acad Sci USA 1990,87, 1744. Inset: Competition between pP53-05 and p53AD for GST-MDM2, asmonitored by fluorescence polarization analysis. Plot illustrates thefraction of p53AD-Flu (10 nM) bound to GST-MDM2 (400 nM) at equilibriumas a function of added pP53-05 (4.5 μM-0.18 μM). K_(i) was calculatedusing the Cheng-Prusoff equation.

FIG. 4—Circular dichroism analysis of pP53-05 and p53AD secondarystructure. Spectra were acquired in 0.5×PBS at 25° C. using a Aviv Model62DS spectrometer. (a) Plots illustrate the CD spectra of pP53-05 at2.75 μM () and 6.75 μM (◯) and p53AD at 3 μM (□). Each data setrepresents the average of 10 scans. Spectra were background correctedbut were not smoothed. (b) Temperature dependence of the CD spectrum ofpP53-05. Θ_(MRE) is in units of deg·cm²·dmol⁻¹.

FIG. 5—Structures of (A) the PKA catalytic subunit bound to PKI₅₋₂₄(Zheng, et al., Acta Cryst 1993, D49, 362-5) and (B) the natural productK252a and K252a-Δ.

FIG. 6—Design of PKA inhibitors. Residues that contribute significantlyto PKA inhibition are in red; residues that contribute to aPP foldingare in blue (α-helix) or yellow (PPII helix).

FIG. 7—Affinity and inhibitory potency of PKA ligands. Fluorescencepolarization analysis of the equilibrium affinity of PKI^(Flu) (black),1^(Flu) (blue) and 2^(Flu) (orange) for PKA in the presence (A) andabsence (B) of 100 μM ATP. Inhibition of the phosphotransferase activityof PKA (red), PKB (black), PKCa (blue), PKG (green), and CamKII (pink)by (C) K252a; (D) PKI-K252a; and (E) 1-K252a.

FIG. 8—Protein grafting applied to the KID^(P)·KIX interaction. (A)Schematic representation of the protein grafting process. In theKID^(P)·KIX complex, the backbone of CREB KID helix B is in blue, thehydrophobic residues of helix B important for CBP KIX binding are inred, the PKA recognition site is in green, and the Ser phosphate moietyis in blue (phosphorous) and white (oxygen). In aPP, residues from theα-helix that form part of the hydrophobic core are in blue and residuesfrom the polyproline helix are in orange. In PPKID Library 1, the Cαatoms at randomized positions are in orange. (B) Library design. Theamino acid sequence of helix B of CREB KID is aligned with the sequenceof the α-helix of aPP. The amino acid sequence of PPKID Library 1 isbelow. Residues important for aPP folding are in blue, the PKArecognition site is in green, and hydrophobic residues of helix Bimportant for binding CBP KIX are in red. Randomized residues arerepresented by X in orange. (C) Comparison of the α-helix-bindingsurfaces of Bcl-X_(L) (left) and CBP KIX (right). Bcl-X_(L) contains adeep (˜7 Å) hydrophobic cleft that recognizes the Bak BH3 α-helix. CBPKIX binds the CREB KID helix B in a shallow depression (<5 Å at thedeepest point) on its surface.

FIG. 9—HisKIX-binding affinity of PPKID and control peptides measured byfluorescence polarization. Serial dilutions of HisKIX were incubatedwith 25-50 nM of fluorescein-labeled peptide (peptide^(Flu)) for 30 minat 25° C. Each point represents an average of three independent samples;the error bars denote standard error. Observed polarization values wereconverted to fraction of peptide^(Flu) bound using P_(min) and P_(max)values derived from the best fit of the polarization data to equation(1). Curves shown are the best fit of fraction of peptide^(Flu) boundvalues to the equilibrium binding equation (2). Fraction ofphosphorylated peptide^(Flu) bound values are indicated with circularsymbols, and fraction of unphosphorylated peptide^(Flu) bound values areindicated with triangular symbols. (A) KID-AB^(P), KID-B^(P), peptideC^(P) and PPKID^(P)1-3. (B) KID-AB^(U), KID-B^(U), peptide C^(U) andPPKID^(U) 1-3. (C)PPKID^(P) 4-5, PPKID^(U) 4-5 and PPKID^(U) 7-8. (D)PPKID6^(U), PPKID6^(P) and PPKID6 S18E.

FIG. 10—Competition between KID-AB^(P) and PPKID4^(P) (solid circle) orPPKID6^(U) (open circle) for binding to HisKIX measured by fluorescencepolarization. Serial dilutions of KID-AB^(P) were incubated with 1.5 μMor 3.0 μM HisKIX and 25 nM fluorescein-labeled PPKID4^(P) or PPKID6^(U)(peptide^(Flu)) for 60 min at 25° C., respectively. Each pointrepresents an average of three independent samples; the error barsdenote standard error. Observed polarization values were converted tofraction of peptide^(Flu) bound using experimentally determined P_(min)and P_(max) values corresponding to the polarization of samplescontaining 25 nM peptide^(Flu) alone and peptide^(Flu) with 1.5 μM or3.0 μM HisKIX, respectively. Curves shown represent the best fit offraction of peptide^(Flu) bound values to equation (3). The closeagreement between the K_(d) of the KID-AB^(P)·HisKIX complex and theIC₅₀ values determined here provides evidence that the fluorescein tagappended to KID-AB^(P) contributes neither positively nor negatively tothe stability of the KID-AB^(P)·HisKIX complex.

FIG. 11—Affinity of PPKID4^(P) (blue circle), PPKID6^(U) (blue triangle)and KID-AB^(P) (red circle) for GST-KIX_(Y650A) measured by fluorescencepolarization. Serial dilutions of GST-KIX_(Y650A) were incubated with 25nM of fluorescein-labeled peptide (peptide^(Flu)) for 30 min at 25° C.Each point represents an average of three independent samples; the errorbars denote standard error. Observed polarization values were convertedto fraction of peptide^(Flu) bound using P_(min) and P_(max) valuesderived from the best fit of the polarization data to equation (1).Curves shown are the best fit of fraction of peptide^(Flu) bound valuesto the equilibrium binding equation (2).

FIG. 12—Specificity of protein surface recognition by PPKID and controlpeptides measured by fluorescence polarization. Binding reactionscontaining serially diluted target protein and 25-50 nM offluorescein-labeled peptides (peptide^(Flu)) were incubated for 30 minat 25° C. Each point represents the average polarization of two to threeindependent samples; error bars denote standard error. Observedpolarization values were converted to fraction of peptide^(Flu) boundusing P_(min) and P_(max) values derived from the best fit of thepolarization data to equation (1). Curves shown are the best fit offraction of peptide^(Flu) bound values to the equilibrium bindingequation (2). (A) Plot illustrating the polarization offluorescently-labeled PPKID4^(P), PPKID6^(U), peptide C^(P) and peptideC^(U) molecules as a function of target protein (carbonic anhydrase IIor HisKIX) concentration. Circular and triangular symbols indicate thatHisKIX was used as the target protein; the symbols are colored as inFIG. 9 with the exception of the points for peptide C^(U), which are inorange for clarity. Square symbols indicate that carbonic anhydrase wasused as the target protein. (B) Plot illustrating the polarization offluorescently-labeled PPKID4^(P), PPKID6^(U) and peptide C^(P) moleculesas a function of target protein (calmodulin or HisKIX) concentration.Circular and triangular symbols indicate that HisKIX was used as thetarget protein, and the symbols are colored as in FIG. 9. Square symbolsindicate that calmodulin was used as the target protein.

FIGS. 13A-I—Binding isotherms illustrating the equilibrium affinities ofPPKID4^(P), PPKID6^(U) and KID-AB^(P) for CBP KIX variants as determinedby fluorescence polarization analysis at 25° C. Each plot illustratesthe fraction of 25 nM (A-C) KID-AB^(P), (D-F) PPKID4^(P), or (G-I)PPKID6^(U) bound as a function of the concentration of CBP KIX variant(M). Observed polarization values were converted to fraction ofligand^(Flu) bound using P_(min) and P_(max) values derived from thebest fit of the polarization data to equation (1). Curves shownrepresent the best fit of the data to equation (2). Phosphorylatedligands are indicated with circles, whereas unphosphorylated ligands areindicated by triangles. Each point represents an average of threeindependent trials; error bars denote standard error.

FIGS. 14A-B—Close-up view of: (A) phosphoserine and (B) hydrophobiccontacts in the KID-AB^(P)·CBP KIX complex. The backbones of KID-AB^(P)and CBP KIX are depicted as red and blue ribbons, respectively; the sidechains of Y658, K662, L603, K606 and Y650 (from CBP KIX) and S133, L138,L141 and A145 (from KID-AB^(P)) are shown explicitly.

FIG. 15—Close-up view of packing between residues on the α-helix andPPII helix in the aPP hydrophobic core.

FIGS. 16A-B—Affinities of PPKID4^(P) variants for CBP KIX as determinedby equilibrium fluorescence polarization analysis. Each point representsan average of three independent trials. Observed polarization valueswere converted to fraction of ligand^(Flu) bound using P_(min) andP_(max) value derived from the best fit of the polarization data toequation (1). Curves shown are the best fit of fraction of ligand^(Flu)bound values to the equilibrium binding equation (2). A) Bindingisotherms for PPKID4P variants L17A, F20A, L24A, Y27A and L28A. B)Binding isotherms for PPKID4P variants P2A, P2Z, P5A, P5Z, P8A and P8Z.Z indicates the substitution of sarcosine in place of alanine.

FIGS. 17A-C—(a) Transcriptional activation mediated by Gal4 DBD fusionsof PPKID4, PPKID6 and KID-AB in HEK293 cells in the absence (b) orpresence (c) of excess p300. The potency of each activation domain (foldactivation) was determined by dividing the R values measured in cellstransfected with a Ga4 DBD fusion by the R value measured in cellstransfected with the pAL1 control. The R value refers to the ratio ofthe activity of firefly and Rinella luciferase measured using theDual-Luciferase® Reporter Assay System (Promega). Bars and standarderror represent the results from at least 3 independent trials. Whereindicated, 5 μM forskolin was added to the culture media 6 h prior toharvesting cells. When indicated, cells were also transfected with anexpression vector encoding full-length p300 under control of the CMVpromoter (25 ng).

FIG. 18—Transcriptional inhibition by PPKID4^(P) peptide in mammaliancells. For each peptide, 5 ng of the Gal4 DNA-binding domain fusionconstruct. For each peptide, HEK293 cells were transfected with 5 ng ofthe Gal4 DBD fusion construct and indicated amount of PPKID4 vector(PPKID4 expressed without Gal4 DBD) and assayed for activation. Bars andstandard error represent the results from at least 3 independent trials.Firefly luciferase values were normalized to an internal control(luciferase values from promoterless Renilla luciferase vector) tocorrect for transfection efficiency. Fold activation representsnormalized luciferase relative to values for Gal4 DBD alone under thesame. Where phosphorylation is indicated, 5 μM forskolin was added tomedia 6 hours before harvesting cells.

DETAILED DESCRIPTION Definitions

As used herein, the term “binding” refers to the specific association orother specific interaction between two molecular species, such as, butnot limited to, protein-DNA interactions and protein-proteininteractions. The specific association can be, for example, betweenproteins and their DNA targets, receptors and their ligands, enzymes andtheir substrates. It is contemplated that such association is mediatedthrough specific sites on each of the two interacting molecular species.Binding is mediated by structural and/or energetic components, thelatter comprising the interaction of molecules with opposite charges.

As used herein, the term “binding site” refers to the reactive region ordomain of a macromolecule that directly participate in its specificbinding with another molecule. For example, when referring to thebinding site on a protein or nucleic acid, binding occurs as a result ofthe presence of specific amino acids or nucleotide sequence,respectively, that interact with the other molecule and, collectively,are referred to as a “binding site.”

As used herein, the term “exposed on the alpha helix domain” means thatan amino acid substituted, for example, into the avian pancreaticpolypeptide is available for association or interaction with anothermolecule and are not otherwise bound to or associated with another aminoacid residue on the avian pancreatic polypeptide. This term is usedinterchangeably with the term “solvent-exposed alpha helical face”throughout the specification.

As used herein, the terms “miniature protein” or “miniprotein” refers toa relatively small protein containing at least a protein scaffold andone or more additional domains or regions that help to stabilize itstertiary structure. The term “miniature protein” includes any variantsof the miniature protein (e.g., mutants, fragments, fusions, andpeptidomimetic forms) that retain a useful activity. An exemplaryprotein scaffold is an avian pancreatic polypeptide (aPP). In certainspecific embodiments, a miniature protein is referred to as “modifiedaPP” or “modified polypeptide.”

As used herein, the term “modulate” refers to an alteration in theassociation between two molecular species, for example, theeffectiveness of a biological agent to interact with its target byaltering the characteristics of the interaction in a competitive ornon-competitive manner.

As used herein, the term “protein” refers to any of a group of complexorganic compounds which contain carbon, hydrogen, oxygen, nitrogen andusually sulphur, the characteristic element being nitrogen and which arewidely distributed in plants and animals. Twenty different amino acidsare commonly found in proteins and each protein has a unique,genetically defined amino acid sequence which determines its specificshape and function. The term “protein” is generally used hereininterchangeably with the terms peptide and polypeptide.

As used herein, the term “protein scaffold” refers to a region or domainof a relatively small protein, such as a miniature protein, that has aconserved tertiary structural motif which can be modified to display oneor more specific amino acid residues in a fixed conformation.

Miniature Proteins

The present invention provides engineered miniature proteins thatassociate with (i.e., or bind to) specific sequences of DNA or otherproteins and also provides methods for designing and making theseminiature proteins. These miniature proteins bind, for example, to DNAor other proteins with high affinity and selectivity. Schematically, theinvention involves a technique that the inventors have designated asprotein grafting (see, e.g., FIGS. 2, 6, and 8). In one aspect, thistechnique identifies critical binding site residues from a globularprotein that participate in binding-type association between thatprotein and its specific binding partners, then these residues aregrafted onto a small but stable protein scaffold. The preferred proteinscaffolds of the invention comprise members of the pancreatic fold (PPfold) protein family, particularly the avian pancreatic polypeptide(aPP). Thus, in certain specific embodiments, the miniature protein isreferred to a modified polypeptide such as a modified aPP.

The PP fold protein scaffolds of the invention generally containthirty-six amino acids and are the smallest known globular protein. Forexample, an avian pancreatic polypeptide (aPP) sequence is designed asSEQ ID NO: 36. Despite their small size, PP fold proteins are stable andremain folded under physiological conditions. The preferred PP foldprotein scaffolds of the invention consist of two anti-parallel helices,an N-terminal type II polyproline helix (PPII) between amino acidresidues two and eight and an alpha-helix between residues 14 and 31and/or 32. The stability of the PP fold protein scaffolds of theinvention derives predominantly from interactions between hydrophobicresidues on the interior face of the alpha-helix at positions 17, 20,24, 27, 28, 30 & 31 and the residues on the two edges of the polyprolinehelix at positions 2, 4, 5, 7 & 8. In general, the residues responsiblefor stabilizing it tertiary structure are not substituted in order tomaintain the tertiary structure of the miniature protein or arecompensated for using phage display.

In certain embodiments, two or more of the critical binding siteresidues of, for example, a selected globular protein are grafted ontothe protein scaffold in positions which are not essential in maintainingtertiary structure, preferably on the solvent-exposed alpha helicalface. In one preferred embodiment, six or more of such binding siteresidues are grafted onto the protein scaffold. In a more preferredembodiment, eight or more of such binding site residues are grafted ontothe protein scaffold. In an even more preferred embodiment, ten or moreof such binding site residues are grafted onto the protein scaffold. Ina most preferred embodiment, twelve or more of such binding siteresidues are grafted onto the protein scaffold. Preferred positions forgrafting these binding site residues on the protein scaffold include,but are not limited to, positions on the solvent-exposed alpha-helicalface of aPP. Substitutions of binding site residues may be made,although they are less preferred, for residues involved in stabilizingthe tertiary structure of the miniature protein.

The skilled artisan will readily recognize that it is not necessary thatactual substitution of the grafted residues occur on the proteinscaffold. Rather it is necessary that a peptide be identified, through,for example, phage display, that comprises a polypeptide constituting aminiature protein having the association characteristics of the presentinvention. Such peptides may be produced using any conventional means,including, but not limited to synthetic and recombinant techniques.

Members of the PP fold family of protein scaffolds which arecontemplated by the present invention include, but are not limited to,avian pancreatic polypeptide (aPP), Neuropeptide Y, lower intestinalhormone polypeptide and pancreatic peptide. In the most preferredembodiment, the protein scaffold comprises the PP fold protein, avianpancreatic polypeptide (SEQ ID NO: 06) (see, e.g., Blundell et al.,(1981) Proc. Natl. Acad. Sci. USA 78, 4175-4179; Tonan et al., (1990)Biochemistry 29, 4424-4429). aPP is a PP fold polypeptide characterizedby a short (eight residue) amino-terminal type II polyproline helixlinked through a type I beta turn to an eighteen residue alpha-helix.Because of its small size and stability, aPP is an excellent proteinscaffold for, e.g., protein grafting of alpha-helical recognitionepitopes.

DNA-Binding Miniature Proteins

In another aspect, the present invention encompasses miniature proteinsthat bind to specific DNA sequences and further encompasses methods formaking and using such miniature proteins. In some embodiments, these DNAsequences comprise sites for known proteins that bind to that specificDNA sequence (contemplated known proteins would be, e.g., a promotor orregulator). For example, in the design of a DNA-binding miniatureprotein, the amino acid residues of a known protein that participate inbinding or other association of the protein to that particular DNAsequence are identified.

In some embodiments of the present invention, the relevant bindingresidues are identified using three-dimensional models of a protein orprotein complex based on crystallographic studies while in otherembodiments they are identified by studies of deletion or substitutionmutants of the protein. The residues that participate in binding of theprotein to the specific DNA sequence are then grafted onto thosepositions of the miniature protein that are not necessary to maintainthe tertiary structure of the protein scaffold to form the DNA-bindingminiature protein. The identification of such positions can readily bedetermined empirically by persons skilled in the art. Other embodimentsof the present invention involve the screening of a library of modifiedminiproteins that contain peptide species capable of specificassociation or binding to that specific DNA (or, in other cases,protein) sequence or motif.

Generally, it is contemplated that any potential binding site on a DNAsequence can be targeted using the DNA binding miniature proteins of theinvention. Preferred embodiments include helical structures which bindto the DNA binding site. In some embodiments, the binding involves abasic region leucine zipper (bZIP) structure (Konig & Richmond, (1995)J. Mol. Biol. 254, 657-667) while in other embodiments the structureinvolves a basic-helix-loop-helix (bHLH) structure (Shimizu et al.,(1997) EMBO J. 16, 4689-4697). In another embodiment, the bindinginvolves a structure like those found in homeodomain proteins (Scott &Weimer, (1984) Proc. Natl. Acad. Sci. 81, 4115-4119). Preferred bZIPstructures include, but are not limited to, those found in GCN4 andC/EBP-delta (Suckow et al., (1993) EMBO J. 12, 1193-1200) whilepreferred bHLH structures include, but are not limited to, those foundin Max (Ferre-D'Amare et al., (1993) Nature 363, 38-45), Myc and MyoD(Ma et al., (1994) Cell 77, 451-459). Preferred homeodomain structuresinclude, but are not limited to, those found in the Q50 engrailedvariant protein (Kissinger et al., (1990) Cell 63, 579-590).

In one embodiment, the invention encompasses a DNA-binding miniatureprotein that binds to the cAMP Response Element (CRE) half-site promotorDNA sequence (ATGAC) (SEQ ID NO: 65). Essential residues for binding areidentified from the protein GCN4 which is a bZIP protein which binds tothis sequence. These residues are identified by utilizing thethree-dimensional structure of the GCN4 protein which bind to the hsCREand grafting these residues onto the protein scaffold. By graftingvarious combinations of residues on the solvent-exposed alpha-helicalface or domain of aPP which are essential to binding of GCN4 (SEQ ID NO:7) to the CRE half site (hsCRE), a series of polyproline helix-basicregion (PPBR^(SR)) molecules containing most or all of the DNA-contactresidues of GCN4 and most or all of the folding residues of aPP isgenerated. This procedure generated three positions (Tyr27, Leu28 andVal30) where essential DNA-contact and aPP-folding residues occupied asingle position on the helix.

Examples of the DNA-binding miniature proteins which bind to hsCREinclude, but are not limited to, the amino acid sequences depicted inSEQ ID NO: 11 (PPBR2^(SR)), 12 (PPBR4^(SR)), 13 (G₂₇) & 14(PPBR4Δ^(SR)).

In another embodiment, protein grafting was used for the design of aminiature protein whose DNA binding properties mimic those of theCCAAT/enhancer protein C/EBP-delta. C/EBP-delta is a member of the C/EBPsub-family of bZIP transcription factors that includes C/EBP-alpha,C/EBP-beta, C/EBP-gamma, C/EBP-delta and C/EBP-epsilon. Although C/EBPproteins are members of the bZIP superfamily, they differ from CGN4 atseveral residues within the DNA recognition helix. In particular,D/EBP-delta and GCN4 differ at two of six residues that contact bases orsugars and three of six residues that contact phosphates in allpublished structures of GCN4 DNA complexes. These changes, as well asthe substitution of tyrosine or alanine at position fifteen, contributeto the preferred interaction of C/EBP proteins with the C/EBP site(ATTGCGCAAT) (SEQ ID NO: 67) over the CRE site (ATGACGTCAT) (SEQ ID NO:68) recognized by GCN4.

For the design of PPEBP (polyproline-enhancer binding protein) accordingto the present invention, the first step in the grafting protocol isalignment of the alpha-helix of aPP (residues 14-36) with thealpha-helical region of the protein of interest. Alignment of the aPPalpha-helix with residues 187-221 (the DNA-binding basic segment) ofhuman C/EBP-delta identified three conflict positions (27, 28 & 30according to the aPP numbering system) where DNA-contact residues withinC/EBP-delta and folding residues within aPP occupied the same positionon the helix. The PPEBP1^(SR) (SEQ ID NO: 47) miniature protein of theinvention contains arginine residues derived from C/EBP-delta atpositions 27, 28 & 30 to preserve binding affinity because high-affinityDNA recognition by PPEBP miniature proteins is enhanced by retention ofDNA-contact residues at these positions despite the concomitant loss infolding energy. In addition, tyrosine, asparagine and valine residuesare substituted at positions 15, 23 & 26, respectively to fosterspecific recognition of the C/EBP half site ATTGC (hsCEBP). Finally analanine residue is inserted at position 31 in place of the potentiallycore-disrupting and complex-destabilizing aspartate found in C/EBP-deltaand in place of the helix destabilizing valine present at this positionof aPP.

Examples of the DNA-binding miniature proteins which bind to the C/EBPsite include, but are not limited to, the amino acid sequences depictedin SEQ ID NO: 47 (PPEBP1^(SR)), 48 (PPEBP2^(SR)) and 49 (EBP1^(SR)).

Methods of Producing Miniature Proteins Using Phage Display

In some embodiments, a miniature protein is produced and selected usinga phage display method (McCafferty et al., (1990) Nature 348, 552-554).In such a method, display of recombinant miniature proteins on thesurface of viruses which infect bacteria (bacteriophage or phage) makeit possible to produce soluble, recombinant miniature proteins having awide range of affinities and kinetic characteristics. To display theminiature proteins on the surface of phage, a synthetic gene encodingthe miniature protein is inserted into the gene encoding a phage surfaceprotein (pIII) and the recombinant fusion protein is expressed on thephage surface (McCafferty et al., (1990) Nature 348, 552-554; Hoogenboomet al., (1991) Nucleic Acids Res. 19, 4133-4137). Variability isintroduced into the phage display library to select for miniatureproteins which not only maintain their tertiary, helical structure butwhich also display increased affinity for a preselected target becausethe critical (or contributing but not critical) binding residues areoptimally positioned on the helical structure.

Since the recombinant proteins on the surface of the phage arefunctional, phage bearing miniature proteins that bind withhigh-affinity to a particular target DNA or protein can be separatedfrom non-binding or lower affinity phage by antigen affinitychromatography. Mixtures of phage are allowed to bind to the affinitymatrix, non-binding or lower affinity phage are removed by washing, andbound phage are eluted by treatment with acid or alkali. Depending onthe affinity of the miniature protein for its target, enrichment factorsof twenty-fold to a million-fold are obtained by a single round ofaffinity selection. By infecting bacteria with the eluted phage,however, more phage can be grown and subjected to another round ofselection. In this way, an enrichment of a thousand-fold in one roundbecomes a million-fold in two rounds of selection. Thus, even whenenrichments in each round are low (Marks et al., (1991) J. Mol. Biol,222, 581-597), multiple rounds of affinity selection leads to theisolation of rare phage and the genetic material contained within whichencodes the sequence of the domain or motif of the recombinant miniatureprotein that binds or otherwise specifically associates with it bindingtarget.

In various embodiments of the invention, the methods disclosed hereinare used to produce a phage expression library encoding miniatureproteins capable of binding to a DNA or to a protein that has alreadybeen selected using the protein grafting procedure described above. Insuch embodiments, phage display can be used to identify miniatureproteins that display an even higher affinity for a particular targetDNA or protein than that of the miniature proteins produced without theaid of phage display. In yet another embodiment, the inventionencompasses a universal phage display library that can be designed todisplay a combinatorial set of epitopes or binding sequences to permitthe recognition of nucleic acids, proteins or small molecules by aminiature protein without prior knowledge of the natural epitope orspecific binding residues or motifs natively used for recognition andassociation.

Various structural modifications also are contemplated for the presentinvention that, for example, include the addition of restriction enzymerecognition sites into the polynucleotide sequence encoding theminiature protein that enable genetic manipulation of these genesequences. Accordingly, the re-engineered miniature proteins can beligated, for example, into an M13-derived bacteriophage cloning vectorthat permits expression of a fusion protein on the phage surface. Thesemethods allow for selecting phage clones encoding fusion proteins thatbind a target ligand and can be completed in a rapid manner allowing forhigh-throughput screening of miniature proteins to identify theminiature protein with the highest affinity and selectivity for aparticular target.

According to the methods of the invention, a library of phage displayingmodified miniature proteins is incubated with the immobilized target DNAor proteins to select phage clones encoding miniature proteins thatspecifically bind to or otherwise specifically associate with theimmobilized DNA or protein. This procedure involves immobilizing aoligonucleotide or polypeptide sample on a solid substrate. The boundphage are then dissociated from the immobilized oligonucleotide orpolypeptide and amplified by growth in bacterial host cells. Individualviral plaques, each expressing a different recombinant miniatureprotein, are expanded to produce amounts of protein sufficient toperform a binding assay. The DNA encoding this recombinant bindingprotein can be subsequently modified for ligation into a eukaryoticprotein expression vector. The modified miniature protein, adapted forexpression in eukaryotic cells, is ligated into a eukaryotic proteinexpression vector.

Phage display methods that can be used to make the miniature proteins ofthe present invention include those disclosed in Brinkman et al., (1995)J. Immunol. Methods 182, 41-50; Ames et al., (1995) J. Immunol. Methods184:177-186; Kettleborough et al., (1994) Eur. J. Immunol. 24, 952-958;Persic et al., (1997) Gene 187, 9-18; Burton et al., (1994) Adv.Immunol. 57, 191-280; U.S. Pat. Nos. 5,698,426; 5,223,409; 5,403,484;5,580,717; 5,427,908; 5,750,753; 5,821,047; 5,571,698; 5,427,908;5,516,637; 5,780,225; 5,658,727; 5,733,743, 5,837,500 & 5,969,108.

Protein-Binding Miniature Proteins and Variants thereof.

The invention encompasses miniature proteins that bind to other proteinsand methods for making these miniature proteins. The binding of theminiature proteins modulates protein-protein and/or protein-ligandinteractions. Thus, in some embodiments, the binding blocks theassociation (or specific binding) of ligands and receptors. The ligandcan be either another protein but also can be any other type of moleculesuch as a chemical substrate. In one embodiment of the presentinvention, making the protein-binding miniature protein of the inventioninvolves identifying the amino acid residues which are essential tobinding of the ligand protein to its target receptor protein. In someembodiments, these essential residues are identified usingthree-dimensional models of a protein or protein complex which binds toor interacts with another protein based on crystallographic studieswhile in other embodiments they are identified by studies of deletion orsubstitution mutants of the protein. The residues that participate inbinding of the protein to are then grafted onto those positions whichare not necessary to maintain the tertiary structure of the proteinscaffold to form the protein-binding miniature protein.

The structure of any protein which binds to another protein can be usedto derive the protein-binding miniature proteins of the invention.Preferred embodiments include helical structures such as those involvedin protein-protein interactions between Fos and Jun (Kouzarides & Ziff,(1988) Nature 336, 646-651); Bcl-2 and Bak (Sattler et al., (1997)Science 275, 983-986); CBP-KIX and CREB-KID (Radhakrishnan et al.,(1997) Cell 91, 741-752); p53 and MDM2 (Kussie et al., (1996) Science274, 948-953); and a protein kinase and a protein kinase inhibitor (PKI)(Glass et al., (1989) J Biol Chem 264, 14579-84). In some embodiments,the binding involves coiled coil protein structures and/or leucinezippers.

In one embodiment of the invention, the methods disclosed herein areused to produce a miniature protein that binds to the Bcl-2 or Bcl-X_(L)proteins (Sattler et al., (1997) Science 275, 983-986). In this method,the protein grafting procedure described herein was applied to theBak-BH3 binding domain to design a miniature protein capable of bindingto Bcl-X_(L). In this procedure, the primary sequence of a protein ofinterest is aligned with residues in the alpha helix of aPP. Allpossible alignments of the primary sequence of positions 74-92 of Bakwith aPP are assessed in two ways. First, the number of conflicts in aprimary sequence alignment between residues important for hydrophobiccore formation or maintenance of aPP helix dipole, and residues in Bakimportant for binding Bcl-X_(L) was considered. Alignments with a largenumber of conflicts are eliminated as they would force selection betweensequences that were well folded or have high affinity, but make itdifficult to isolate a molecule with both these properties.

Structural models of the aPP based peptides that are associated orcomplexed with the BH3 domain of Bcl-X_(L) in each of the alignments areevaluated for unfavorable interactions or steric clashes between theVanderWaals surface of Bcl-X_(L) and the backbone of the aPP scaffold.Structural models with multiple unfavorable interactions or stericclashes are eliminated from further consideration.

An alignment is identified with only a single conflict where structuralmodeling suggested no steric clashes. A phage display expression libraryof chimeric peptides ultimately was based on this alignment. Theresulting library of peptides was displayed on the surface of M13 phageand used in selection and isolation of miniature proteins that bind Bclwith high-affinity. Examples of bcl2-binding miniature proteins include,but are not limited to, those sequences having a carboxyl portionsequence as depicted in SEQ ID NO: 23 (4100), 24 (4101), 25 (4099) or 26(4102). The amino terminal portion of the miniature proteins isunderstood to derive from the amino terminal portion (e.g., residues1-19) of the aPP (SEQ ID NO: 6).

In another embodiment of the invention, the methods of the invention areused to produce a miniature protein that binds to the human doubleminute two (MDM2). The alpha-helical segments of p53 and aPP werealigned to identify three critical MDM2 contact residues (e.g.,positions 22, 26, and 29) on the exposed alpha-helical face of aPPwithout substituting any aPP residues important for folding. Becausemany p53 residues within the p53 activation domain that interacts withMDM2 display phi and psi angles outside the ideal alpha-helical range,this application of protein grafting introduced diversity at fivepositions along the alpha-helix and the highest affinity ligands wereselected using phage display. Examples of miniature proteins which bindto MDM2 include, but are not limited to, the amino acid sequencesdepicted in FIG. 2 (e.g., pP53-01, pP53-02, pP53-03, pP53-04 andpP53-05).

In another embodiment of the invention, the methods of the invention areused to produce a miniature protein that binds to protein kinase K(PKA). The alpha-helical segments of a PKI and aPP were aligned toidentify critical contact residues on the exposed alpha-helical face ofaPP without substituting any aPP residues important for folding.Examples of miniature proteins which bind to PKA include, but are notlimited to, the amino acid sequences depicted in FIG. 6.

In yet another embodiment of the invention, the methods of the inventionare used to produce a miniature protein that binds to CBP (e.g, the KIXdomain). The alpha-helical segments of a CREB (e.g., the KID domain) andaPP were aligned to identify critical contact residues on the exposedalpha-helical face of aPP without substituting any aPP residuesimportant for folding. Examples of miniature proteins which bind to CBPinclude, but are not limited to, the amino acid sequences depicted inFIG. 8 and Table 1.

In certain embodiments, miniature proteins include fragments, functionalvariants, and modified forms that have similar or the same biologicalactivities of their corresponding wild-type miniature proteins. Toillustrate, miniature proteins of the invention bind to a target proteinand modulate (e.g., activate or inhibit) a function of the targetprotein. In certain cases, target proteins of the miniature proteins areknown to play a role in cell proliferation and differentiation.Therefore, miniature proteins of the invention can be used for treatingor preventing disorders associated with abnormal cell proliferation anddifferentiation (e.g., inflammation, allergy, autoimmune diseases,infectious diseases, and tumors).

In certain embodiments, miniature proteins of the present inventionfurther include conservative variants of the miniature proteins hereindescribed. As used herein, a conservative variant refers to a miniatureprotein comprising alterations in the amino acid sequence that do notsubstantially and adversely affect the binding or association capacityof the protein. A substitution, insertion or deletion is said toadversely affect the miniature protein when the altered sequenceprevents or disrupts a function or activity associated with the protein.For example, the overall charge, structure or hydrophobic-hydrophilicproperties of the miniature protein can be altered without adverselyaffecting an activity. Accordingly, the amino acid sequence can bealtered, for example to render the peptide more hydrophobic orhydrophilic, without adversely affecting the activities of the miniatureprotein.

In certain embodiments, these variants, though possessing a slightlydifferent amino acid sequence than those recited above, will still havethe same or similar properties associated with the miniature proteinssuch as those depicted in SEQ ID NOs: 8, 9, 10, 11, 12, 13, 17, 18, 19,20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 33, 34, 35, 36, 37, 47, 48,49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 70, 71,and 72; and FIGS. 1, 2, 6, 8, and Table 1.

Ordinarily, the conservative substitution variants, will have an aminoacid sequence having at least ninety percent amino acid sequenceidentity with the miniature sequences such as those set forth in SEQ IDNOs: 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,28, 29, 31, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56,57, 58, 59, 60, 61, 62, 63, 64, 70, 71 and 72; and FIGS. 1, 2, 6, 8, andTable 1, more preferably at least ninety-five percent, even morepreferably at least ninety-eight percent, and most preferably at leastninety-nine percent. Identity or homology with respect to such sequencesis defined herein as the percentage of amino acid residues in thecandidate sequence that are identical with the known peptides, afteraligning the sequences and introducing gaps, if necessary, to achievethe maximum percent homology, and not considering any conservativesubstitutions as part of the sequence identity. N-terminal, C-terminalor internal extensions, deletions, or insertions into the peptidesequence shall not be construed as affecting homology.

Thus, the miniature proteins of the present invention include moleculescomprising the amino acid sequence of SEQ ID NOs: 8, 9, 10, 11, 12, 13,17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 33, 34, 35, 36,37, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63,64, 70, 71 and 72; and FIGS. 1, 2, 6, 8, and Table 1; fragments thereofhaving a consecutive sequence of at least about 20, 25, 30, 35 or moreamino acid residues of the miniature proteins of the invention; aminoacid sequence variants of such sequences wherein at least one amino acidresidue has been inserted N- or C-terminal to, or within, the disclosedsequence; amino acid sequence variants of the disclosed sequences, ortheir fragments as defined above, that have been substituted by anotherresidue. Contemplated variants further include those derivatives whereinthe protein has been covalently modified by substitution, chemical,enzymatic, or other appropriate means with a moiety other than anaturally occurring amino acid (for example, a detectable moiety such asan enzyme or radioisotope).

In certain embodiments, the miniature proteins of the present inventioncan be chemically synthesized using techniques known in the art such asconventional Merrifield solid phase f-Moc or t-Boc chemistry.Alternatively, the miniature proteins can be produced (recombinantly orby chemical synthesis).

In certain embodiments, the present invention contemplates makingfunctional variants by modifying the structure of a miniature proteinfor such purposes as enhancing therapeutic efficacy, or stability (e.g.,ex vivo shelf life and resistance to proteolytic degradation in vivo).Such modified miniature proteins when designed to retain at least oneactivity of the wildtype form of the miniature proteins, are consideredfunctional equivalents of the wildtype miniature proteins.

In certain embodiments, the miniature proteins of the present inventioninclude peptidomimetics. As used herein, the term “peptidomimetic”includes chemically modified peptides and peptide-like molecules thatcontain non-naturally occurring amino acids, peptoids, and the like.Peptidomimetics provide various advantages over a peptide, includingenhanced stability when administered to a subject. Methods foridentifying a peptidomimetic are well known in the art and include thescreening of databases that contain libraries of potentialpeptidomimetics. For example, the Cambridge Structural Database containsa collection of greater than 300,000 compounds that have known crystalstructures (Allen et al., Acta Crystallogr. Section B, 35:2331 (1979)).Where no crystal structure of a target molecule is available, astructure can be generated using, for example, the program CONCORD(Rusinko et al., J. Chem. Inf. Comput. Sci. 29:251 (1989)). Anotherdatabase, the Available Chemicals Directory (Molecular Design Limited,Informations Systems; San Leandro Calif.), contains about 100,000compounds that are commercially available and also can be searched toidentify potential peptidomimetics of the miniature proteins.

To illustrate, by employing scanning mutagenesis to map the amino acidresidues of a miniature protein which are involved in binding to anotherprotein, peptidomimetic compounds can be generated which mimic thoseresidues involved in binding. For instance, non-hydrolyzable peptideanalogs of such residues can be generated using benzodiazepine (e.g.,see Freidinger et al., in Peptides: Chemistry and Biology, G. R.Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988), azepine(e.g., see Huffman et al., in Peptides: Chemistry and Biology, G. R.Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988), substitutedgamma lactam rings (Garvey et al., in Peptides: Chemistry and Biology,G. R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988),keto-methylene pseudopeptides (Ewenson et al., (1986) J. Med. Chem.29:295; and Ewenson et al., in Peptides: Structure and Function(Proceedings of the 9th American Peptide Symposium) Pierce Chemical Co.Rockland, Ill., 1985), b-turn dipeptide cores (Nagai et al., (1985)Tetrahedron Lett 26:647; and Sato et al., (1986) J Chem Soc Perkin Trans1:1231), and b-aminoalcohols (Gordon et al., (1985) Biochem Biophys ResCommun 126:419; and Dann et al., (1986) Biochem Biophys Res Commun134:71).

In certain embodiments, the miniature proteins of the invention mayfurther comprise post-translational modifications in addition to anythat are naturally present in the miniature proteins. Such modificationsinclude, but are not limited to, acetylation, carboxylation,glycosylation, phosphorylation, lipidation, and acylation. As a result,the modified miniature proteins may contain non-amino acid elements,such as polyethylene glycols, lipids, poly- or mono-saccharide, andphosphates. Effects of such non-amino acid elements on the functionalityof a miniature protein may be tested by methods such as those describedin the working examples.

In certain aspects, functional variants or modified forms of theminiature proteins include fusion proteins having at least a portion ofthe miniature proteins and one or more fusion domains. Well knownexamples of such fusion domains include, but are not limited to,polyhistidine, Glu-Glu, glutathione S transferase (GST), thioredoxin,protein A, protein G, an immunoglobulin heavy chain constant region(Fc), maltose binding protein (MBP), or human serum albumin. A fusiondomain may be selected so as to confer a desired property. For example,some fusion domains are particularly useful for isolation of the fusionproteins by affinity chromatography. For the purpose of affinitypurification, relevant matrices for affinity chromatography, such asglutathione-, amylase-, and nickel- or cobalt-conjugated resins areused. Many of such matrices are available in “kit” form, such as thePharmacia GST purification system and the QIAexpress™ system (Qiagen)useful with (HIS₆) fusion partners. As another example, a fusion domainmay be selected so as to facilitate detection of the miniature proteins.Examples of such detection domains include the various fluorescentproteins (e.g., GFP) as well as “epitope tags,” which are usually shortpeptide sequences for which a specific antibody is available. Well knownepitope tags for which specific monoclonal antibodies are readilyavailable include FLAG, influenza virus haemagglutinin (HA), and c-myctags. In some cases, the fusion domains have a protease cleavage site,such as for Factor Xa or Thrombin, which allows the relevant protease topartially digest the fusion proteins and thereby liberate therecombinant proteins therefrom. The liberated proteins can then beisolated from the fusion domain by subsequent chromatographicseparation. In certain preferred embodiments, a miniature protein isfused with a domain that stabilizes the miniature protein in vivo (a“stabilizer” domain). By “stabilizing” is meant anything that increasesserum half life, regardless of whether this is because of decreaseddestruction, decreased clearance by the kidney, or other pharmacokineticeffect. Fusions with the Fc portion of an immunoglobulin are known toconfer desirable pharmacokinetic properties on a wide range of proteins.Likewise, fusions to human serum albumin can confer desirableproperties.

Nucleic Acid Molecules Encoding Miniature Proteins

The present invention further provides nucleic acid molecules thatencode the miniature proteins comprising any of the amino acid sequencesof SEQ ID NOs: 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29, 31, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54,55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 70, 71, and 72; and FIGS. 1, 2,6, 8, and Table 1, and the related miniature proteins herein described,preferably in isolated form. As used herein, “nucleic acid” includescDNA and mRNA, as well as nucleic acids based on alternative backbonesor including alternative bases whether derived from natural sources orsynthesized.

As used herein, a nucleic acid molecule is said to be “isolated” whenthe nucleic acid molecule is substantially separated from contaminantnucleic acid encoding other polypeptides from the source of nucleicacid.

The present invention further provides fragments of the encoding nucleicacid molecule. As used herein, a “fragment of an encoding nucleic acidmolecule” refers to a portion of the entire protein encoding sequence ofthe miniature protein. The size of the fragment will be determined bythe intended use. For example, if the fragment is chosen so as to encodean active portion of the protein, the fragment will need to be largeenough to encode the functional region(s) of the protein. Theappropriate size and extent of such fragments can be determinedempirically by persons skilled in the art.

Modifications to the primary structure itself by deletion, addition, oralteration of the amino acids incorporated into the protein sequenceduring translation can be made without destroying the activity of theminiature protein. Such substitutions or other alterations result inminiature proteins having an amino acid sequence encoded by a nucleicacid falling within the contemplated scope of the present invention.

The present invention further provides recombinant DNA molecules thatcontain a coding sequence. As used herein, a recombinant DNA molecule isa DNA molecule that has been subjected to molecular manipulation.Methods for generating recombinant DNA molecules are well known in theart, for example, see Sambrook et al., (1989) Molecular Cloning—ALaboratory Manual, Cold Spring Harbor Laboratory Press. In the preferredrecombinant DNA molecules, a coding DNA sequence is operably linked toexpression control sequences and vector sequences.

The choice of vector and expression control sequences to which one ofthe protein family encoding sequences of the present invention isoperably linked depends directly, as is well known in the art, on thefunctional properties desired (e.g., protein expression, and the hostcell to be transformed). A vector of the present invention may be atleast capable of directing the replication or insertion into the hostchromosome, and preferably also expression, of the structural geneincluded in the recombinant DNA molecule.

Expression control elements that are used for regulating the expressionof an operably linked miniature protein encoding sequence are known inthe art and include, but are not limited to, inducible promoters,constitutive promoters, secretion signals, and other regulatoryelements. Preferably, the inducible promoter is readily controlled, suchas being responsive to a nutrient in the host cell's medium.

In one embodiment, the vector containing a coding nucleic acid moleculewill include a prokaryotic replicon, i.e., a DNA sequence having theability to direct autonomous replication and maintenance of therecombinant DNA molecule extra-chromosomal in a prokaryotic host cell,such as a bacterial host cell, transformed. therewith. Such repliconsare well known in the art. In addition, vectors that include aprokaryotic replicon may also include a gene whose expression confers adetectable marker such as a drug resistance. Typical of bacterial drugresistance genes are those that confer resistance to ampicillin ortetracycline.

Vectors that include a prokaryotic replicon can further include aprokaryotic or bacteriophage promoter capable of directing theexpression (transcription and translation) of the coding gene sequencesin a bacterial host cell, such as E. coli. A promoter is an expressioncontrol element formed by a DNA sequence that permits binding of RNApolymerase and transcription to occur. Promoter sequences compatiblewith bacterial hosts are typically provided in plasmid vectorscontaining convenient restriction sites for insertion of a DNA segmentof the present invention. Any suitable prokaryotic host can be used toexpress a recombinant DNA molecule encoding a protein of the invention.

Expression vectors compatible with eukaryotic cells, preferably thosecompatible with vertebrate cells, can also be used to form a recombinantDNA molecule that contains a coding sequence. Eukaryotic cell expressionvectors are well known in the art and are available from severalcommercial sources. Typically, such vectors are provided containingconvenient restriction sites for insertion of the desired DNA segment.

Eukaryotic cell expression vectors used to construct the recombinant DNAmolecules of the present invention may further include a selectablemarker that is effective in a eukaryotic cell, preferably a drugresistance selection marker. A preferred drug resistance marker is thegene whose expression results in neomycin resistance, i.e., the neomycinphosphotransferase (neo) gene. Southern et al., (1982) J. Mol. Anal.Genet. 1, 327-341. Alternatively, the selectable marker can be presenton a separate plasmid, the two vectors introduced by co-transfection ofthe host cell, and transfectants selected by culturing in theappropriate drug for the selectable marker.

Transformed Host Cells

The present invention further provides host cells transformed with anucleic acid molecule that encodes a miniature protein of the presentinvention. The host cell can be either prokaryotic or eukaryotic.Eukaryotic cells useful for expression of a miniature protein of theinvention are not limited, so long as the cell line is compatible withcell culture methods and compatible with the propagation of theexpression vector and expression of the gene product.

Transformation of appropriate cell hosts with a recombinant DNA moleculeencoding a miniature protein of the present invention is accomplished bywell known methods that typically depend on the type of vector used andhost system employed. With regard to transformation of prokaryotic hostcells, electroporation and salt treatment methods can be employed (see,for example, Sambrook et al., (1989) Molecular Cloning—A LaboratoryManual, Cold Spring Harbor Laboratory Press; Cohen et al., (1972) Proc.Natl. Acad. Sci. USA 69, 2110-2114). With regard to transformation ofvertebrate cells with vectors containing recombinant DNA,electroporation, cationic lipid or salt treatment methods can beemployed (see, for example, Graham et al., (1973) Virology 52, 456-467;Wigler et al., (1979) Proc. Natl. Acad. Sci. USA 76, 1373-1376).

Successfully transformed cells (cells that contain a recombinant DNAmolecule of the present invention), can be identified by well knowntechniques including the selection for a selectable marker. For example,cells resulting from the introduction of a recombinant DNA of thepresent invention can be cloned to produce single colonies. Cells fromthose colonies can be harvested, lysed and their DNA content examinedfor the presence of the recombinant DNA using a method such as thatdescribed by Southern, (1975) J. Mol. Biol. 98, 503-517 or the proteinsproduced from the cell assayed via an immunological method.

Production of Recombinant Miniature Proteins

The present invention further provides methods for producing a miniatureprotein of the invention using nucleic acid molecules herein described.In general terms, the production of a recombinant form of a proteintypically involves the following steps: a nucleic acid molecule isobtained that encodes a protein of the invention, such as the nucleicacid molecule encoding any of the miniature proteins depicted in SEQ IDNO: 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,28, 29, 31, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56,57, 58, 59, 60, 61, 62, 63, 64, 70, 71, and 72; and FIGS. 1, 2, 6, 8,and Table 1. The nucleic acid molecule is then preferably placed inoperable linkage with suitable control sequences, as described above, toform an expression unit containing the protein open reading frame. Theexpression unit is used to transform a suitable host and the transformedhost is cultured under conditions that allow the production of therecombinant miniature protein. Optionally the recombinant miniatureprotein is isolated from the medium or from the cells; recovery andpurification of the protein may not be necessary in some instances wheresome impurities may be tolerated.

Each of the foregoing steps can be done in a variety of ways. Theconstruction of expression vectors that are operable in a variety ofhosts is accomplished using appropriate replicons and control sequences,as set forth above. The control sequences, expression vectors, andtransformation methods are dependent on the type of host cell used toexpress the gene. Suitable restriction sites, if not normally available,can be added to the ends of the coding sequence so as to provide anexcisable gene to insert into these vectors. A skilled artisan canreadily adapt any host/expression system known in the art for use withthe nucleic acid molecules of the invention to produce a recombinantminiature protein.

Methods to Identify Binding Partners

The present invention provides methods for use in isolating andidentifying binding partners of the miniature proteins of the invention.In some embodiments, a miniature protein of the invention is mixed witha potential binding partner or an extract or fraction of a cell underconditions that allow the association of potential binding partners withthe protein of the invention. After mixing, peptides, polypeptides,proteins or other molecules that have become associated with a miniatureprotein of the invention are separated from the mixture. The bindingpartner bound to the protein of the invention can then be removed andfurther analyzed. To identify and isolate a binding partner, the entireminiature protein can be used. Alternatively, a fragment of theminiature protein which contains the binding domain can be used.

As used herein, a “cellular extract” refers to a preparation or fractionwhich is made from a lysed or disrupted cell. A variety of methods canbe used to obtain an extract of a cell. Cells can be disrupted usingeither physical or chemical disruption methods. Examples of physicaldisruption methods include, but are not limited to, sonication andmechanical shearing. Examples of chemical lysis methods include, but arenot limited to, detergent lysis and enzyme lysis. A skilled artisan canreadily adapt methods for preparing cellular extracts in order to obtainextracts for use in the present methods.

Once an extract of a cell is prepared, the extract is mixed with aminiature protein of the invention under conditions in which associationof the miniature protein with the binding partner can occur. A varietyof conditions can be used, the most preferred being conditions thatclosely resemble conditions found in the cytoplasm of a human cell.Features such as osmolarity, pH, temperature, and the concentration ofcellular extract used, can be varied to optimize the association of theprotein with the binding partner.

After mixing under appropriate conditions, the bound complex isseparated from the mixture. A variety of techniques can be utilized toseparate the mixture. For example, antibodies specific to a protein ofthe invention can be used to immunoprecipitate the binding partnercomplex. Alternatively, standard chemical separation techniques such aschromatography and density-sediment centrifugation can be used.

After removal of non-associated cellular constituents found in theextract, the binding partner can be dissociated from the complex usingconventional methods. For example, dissociation can be accomplished byaltering the salt concentration or pH of the mixture.

To aid in separating associated binding partner pairs from the mixedextract, the miniature protein of the invention can be immobilized on asolid support. For example, the miniature protein can be attached to anitrocellulose matrix or acrylic beads. Attachment of the miniatureprotein to a solid support aids in separating peptide-binding partnerpairs from other constituents found in the extract. The identifiedbinding partners can be either a single DNA molecule or protein or acomplex made up of two or more proteins. Alternatively, binding partnersmay be identified using the Alkaline Phosphatase fusion assay accordingto the procedures of Flanagan & Vanderhaeghen, (1998) Annu. Rev.Neurosci. 21, 309-345 or Takahashi et al., (1999) Cell 99, 59-69; theFar-Western assay according to the procedures of Takayama et al., (1997)Methods Mol. Biol. 69, 171-184 or Sauder et al., J. Gen. Virol. (1996)77, 991-996 or identified through the use of epitope tagged proteins orGST fusion proteins.

Alternatively, the nucleic acid molecules encoding a miniature proteinof the invention can be used in a yeast two-hybrid system. The yeasttwo-hybrid system has been used to identify other protein partner pairsand can readily be adapted to employ the nucleic acid molecules hereindescribed (see, e.g., Stratagene Hybrizap® two-hybrid system).

Screening, Diagnostic & Therapeutic Uses

The miniature proteins (including variants thereof) of the invention areparticularly useful for drug screening to identify agents capable ofbinding to the same binding site as the miniature proteins. Theminiature proteins are also useful for diagnostic purposes to identifythe presence and/or detect the levels of DNA or protein that binds tothe miniature proteins of the invention. In one diagnostic embodiment,the miniature proteins of the invention are included in a kit used todetect the presence of a particular DNA or protein in a biologicalsample. The miniature proteins of the invention also have therapeuticuses in the treatment of disease associated with the presence of aparticular DNA or protein. In one therapeutic embodiment, the miniatureproteins can be used to bind to DNA to promote or inhibit transcription,while in another therapeutic embodiment, the miniature proteins bind toa protein, resulting in inhibition or stimulation of the protein.

As described above, miniature proteins bind to target proteins (MDM2,CBP, PKA, a Bcl2 protein, and variants thereof) which are implicated incell proliferation and differentiation. Thus, in certain embodiments,the present invention provides methods of treating cancer in anindividual suffering from a disorder associated with abnormal cellproliferation and differentiation by administering to the individual atherapeutically effective amount of a miniature protein as describedabove. Examples of such disorders include, but are not limited to,inflammation, allergy, autoimmune diseases, infectious diseases, andtumors (cancers).

In other embodiments, the invention provides methods of preventing orreducing the onset of a disorder associated with abnormal cellproliferation and differentiation in an individual through administeringto the individual an effective amount of a miniature protein. Thesemethods are particularly aimed at therapeutic and prophylactictreatments of animals, and more particularly, humans. The term“preventing” is art-recognized, and when used in relation to acondition, such as cancer, is well understood in the art, and includesadministration of a composition which reduces the frequency of, ordelays the onset of, symptoms of a medical condition (here, cancer) in asubject relative to a subject who does not receive the composition.Thus, prevention of cancer includes, for example, reducing the number ofdetectable cancerous growths in a population of patients receiving aprophylactic treatment relative to an untreated control population,and/or delaying the appearance of detectable cancerous growths in atreated population versus an untreated control population, e.g., by astatistically and/or clinically significant amount. Prevention of aninfection includes, for example, reducing the number of diagnoses of theinfection in a treated population versus an untreated controlpopulation, and/or delaying the onset of symptoms of the infection in atreated population versus an untreated control population. Prevention ofpain includes, for example, reducing the magnitude of, or alternativelydelaying, pain sensations experienced by subjects in a treatedpopulation versus an untreated control population.

In certain embodiments of such methods, one or more miniature proteinsthereof can be administered, together (simultaneously) or at differenttimes (sequentially). In addition, a miniature protein can beadministered with another type of compounds for treating cancer (seebelow). The two types of compounds may be administered simultaneously orsequentially.

A wide array of conventional compounds have been shown to haveanti-tumor activities. These compounds have been used as pharmaceuticalagents in chemotherapy to shrink solid tumors, prevent metastases andfurther growth, or decrease the number of malignant cells. Althoughchemotherapy has been effective in treating various types ofmalignancies, many anti-tumor compounds induce undesirable side effects.In many cases, when two or more different treatments are combined, thetreatments may work synergistically and allow reduction of dosage ofeach of the treatments, thereby reducing the detrimental side effectsexerted by each compound at higher dosages. In other instances,malignancies that are refractory to a treatment may respond to acombination therapy of two or more different treatments.

Therefore, the subject miniature protein may be conjointly administeredwith a conventional anti-tumor compound. Conventional anti-tumorcompounds include, merely to illustrate: aminoglutethimide, amsacrine,anastrozole, asparaginase, bcg, bicalutamide, bleomycin, buserelin,busulfan, camptothecin, capecitabine, carboplatin, carmustine,chlorambucil, cisplatin, cladribine, clodronate, colchicine,cyclophosphamide, cyproterone, cytarabine, dacarbazine, dactinomycin,daunorubicin, dienestrol, diethylstilbestrol, docetaxel, doxorubicin,epirubicin, estradiol, estramustine, etoposide, exemestane, filgrastim,fludarabine, fludrocortisone, fluorouracil, fluoxymesterone, flutamide,gemcitabine, genistein, goserelin, hydroxyurea, idarubicin, ifosfamide,imatinib, interferon, irinotecan, ironotecan, letrozole, leucovorin,leuprolide, levamisole, lomustine, mechlorethamine, medroxyprogesterone,megestrol, melphalan, mercaptopurine, mesna, methotrexate, mitomycin,mitotane, mitoxantrone, nilutamide, nocodazole, octreotide, oxaliplatin,paclitaxel, pamidronate, pentostatin, plicamycin, porfimer,procarbazine, raltitrexed, rituximab, streptozocin, suramin, tamoxifen,temozolomide, teniposide, testosterone, thioguanine, thiotepa,titanocene dichloride, topotecan, trastuzumab, tretinoin, vinblastine,vincristine, vindesine, and vinorelbine.

In another related embodiment, the invention contemplates the practiceof the method in conjunction with other anti-tumor therapies such asradiation. As used herein, the term “radiation” is intended to includeany treatment of a neoplastic cell or subject by photons, neutrons,electrons, or other type of ionizing radiation. Such radiations include,but are not limited to, X-ray, gamma-radiation, or heavy ion particles,such as alpha or beta particles. Additionally, the radiation may beradioactive.

Administration and Pharmaceutical Formulations

Miniature proteins (including variants thereof) of the present inventioncan be administered in various forms, depending on the disorder to betreated and the age, condition, and body weight of the patient, as iswell known in the art. For example, where the miniature proteins are tobe administered orally, they may be formulated as tablets, capsules,granules, powders, or syrups; or for parenteral administration, they maybe formulated as injections (intravenous, intramuscular, orsubcutaneous), drop infusion preparations, or suppositories. Forapplication by the ophthalmic mucous membrane route, they may beformulated as eye drops or eye ointments. These formulations can beprepared by conventional means, and, if desired, the active ingredientmay be mixed with any conventional additive, such as an excipient, abinder, a disintegrating agent, a lubricant, a corrigent, a solubilizingagent, a suspension aid, an emulsifying agent, or a coating agent.Although the dosage will vary depending on the symptoms, age and bodyweight of the patient, the nature and severity of the disorder to betreated or prevented, the route of administration and the form of thedrug, in general, a daily dosage of from 0.01 to 2000 mg of the compoundis recommended for an adult human patient, and this may be administeredin a single dose or in divided doses.

The precise time of administration and/or amount of the agent that willyield the most effective results in terms of efficacy of treatment in agiven patient will depend upon the activity, pharmacokinetics, andbioavailability of a particular compound, physiological condition of thepatient (including age, sex, disease type and stage, general physicalcondition, responsiveness to a given dosage, and type of medication),route of administration, etc. However, the above guidelines can be usedas the basis for fine-tuning the treatment, e.g., determining theoptimum time and/or amount of administration, which will require no morethan routine experimentation consisting of monitoring the subject andadjusting the dosage and/or timing.

The phrase “pharmaceutically acceptable carrier” as used herein means apharmaceutically acceptable material, composition or vehicle, such as aliquid or solid filler, diluent, excipient, solvent or encapsulatingmaterial, involved in carrying or transporting the subject chemical fromone organ or portion of the body, to another organ or portion of thebody. Each carrier must be “acceptable” in the sense of being compatiblewith the other ingredients of the formulation and not injurious to thepatient.

Formulations useful in the methods of the present invention includethose suitable for oral, nasal, topical (including buccal andsublingual), rectal, vaginal, aerosol, and/or parenteral administration.The formulations may conveniently be presented in unit dosage form andmay be prepared by any methods well known in the art of pharmacy. Theamount of active ingredient which can be combined with a carriermaterial to produce a single dosage form will vary depending upon thehost being treated and the particular mode of administration. The amountof active ingredient which can be combined with a carrier material toproduce a single dosage form will generally be that amount of thecompound which produces a therapeutic effect. Generally, out of onehundred percent, this amount will range from about 1 percent to aboutninety-nine percent of active ingredient, preferably from about 5percent to about 70 percent, most preferably from about 10 percent toabout 30 percent.

Formulations suitable for oral administration may be in the form ofcapsules, cachets, pills, tablets, lozenges (using a flavored basis,usually sucrose and acacia or tragacanth), powders, granules, or as asolution or a suspension in an aqueous or non-aqueous liquid, or as anoil-in-water or water-in-oil liquid emulsion, or as an elixir or syrup,or as pastilles (using an inert base, such as gelatin and glycerin, orsucrose and acacia) and/or as mouthwashes, and the like, each containinga predetermined amount of a therapeutic agent as an active ingredient. Acompound may also be administered as a bolus, electuary or paste.

Liquid dosage forms for oral administration include pharmaceuticallyacceptable emulsions, microemulsions, solutions, suspensions, syrups,and elixirs. In addition to the active ingredient, the liquid dosageforms may contain inert diluents commonly used in the art, such as, forexample, water or other solvents, solubilizing agents, and emulsifierssuch as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethylacetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3-butyleneglycol, oils (in particular, cottonseed, groundnut, corn, germ, olive,castor, and sesame oils), glycerol, tetrahydrofuryl alcohol,polyethylene glycols, and fatty acid esters of sorbitan, and mixturesthereof.

Formulations which are suitable for vaginal administration also includepessaries, tampons, creams, gels, pastes, foams, or spray formulationscontaining such carriers as are known in the art to be appropriate.Dosage forms for the topical or transdermal administration of atherapeutic agent include powders, sprays, ointments, pastes, creams,lotions, gels, solutions, patches, and inhalants. The active componentmay be mixed under sterile conditions with a pharmaceutically acceptablecarrier, and with any preservatives, buffers, or propellants which maybe required.

The therapeutic agent can be alternatively administered by aerosol. Thisis accomplished by preparing an aqueous aerosol, liposomal preparation,or solid particles containing the compound. A nonaqueous (e.g.,fluorocarbon propellant) suspension could be used. Sonic nebulizers arepreferred because they minimize exposing the agent to shear, which canresult in degradation of the compound. Ordinarily, an aqueous aerosol ismade by formulating an aqueous solution or suspension of the agenttogether with conventional pharmaceutically acceptable carriers andstabilizers.

Transdermal patches have the added advantage of providing controlleddelivery of an therapeutic agent to the body. Such dosage forms can bemade by dissolving or dispersing the agent in the proper medium.Absorption enhancers can also be used to increase the flux of thetherapeutic agent across the skin. The rate of such flux can becontrolled by either providing a rate controlling membrane or dispersingthe peptidomimetic in a polymer matrix or gel.

Pharmaceutical compositions of this invention suitable for parenteraladministration comprise one or more miniature proteins in combinationwith one or more pharmaceutically acceptable sterile isotonic aqueous ornonaqueous solutions, dispersions, suspensions or emulsions, or sterilepowders which may be reconstituted into sterile injectable solutions ordispersions just prior to use, which may contain antioxidants, buffers,bacteriostats, solutes which render the formulation isotonic with theblood of the intended recipient or suspending or thickening agents.

In some cases, in order to prolong the effect of a drug, it is desirableto slow the absorption of the drug from subcutaneous or intramuscularinjection. This may be accomplished by the use of a liquid suspension ofcrystalline or amorphous material having poor water solubility. The rateof absorption of the drug then depends upon its rate of dissolutionwhich, in turn, may depend upon crystal size and crystalline form.Alternatively, delayed absorption of a parenterally administered drugform is accomplished by dissolving or suspending the drug in an oilvehicle.

These miniature proteins may be administered to humans and other animalsfor therapy by any suitable route of administration, including orally,nasally, as by, for example, a spray, rectally, intravaginally,parenterally, intracisternally, and topically, as by powders, ointmentsor drops, including buccally and sublingually.

EXAMPLES

Without further description, it is believed that a person of ordinaryskill in the art can, using the preceding description and the followingillustrative examples, make and utilize the compounds of the presentinvention and practice the claimed methods. The following workingexamples therefore, specifically point out preferred embodiments of thepresent invention, and are not to be construed as limiting in any waythe remainder of the disclosure.

Example 1 Synthesis of DNA-Binding Miniature Proteins

Polypeptides constituting miniature proteins were prepared using solidphase methodology and contain a carboxy-terminal amide and a free aminoterminus unless otherwise indicated. High performance liquidchromatography (HPLC) was performed on either a Waters 600E MultisolventDelivery System with a Waters 490E multiwavelength detector or a RaininDynamax SD-200 Solvent Delivery System with a Rainin Dynamax PDA-2 DiodeArray Detector.

Solid phase peptide synthesis was performed on a Perseptive BioSearch9600 peptide synthesizer. Standard research grade argon (ConnecticutAirGas) was passed through an OxyClear oxygen scrubber beforeintroduction to the synthesizer. HATU(O-(7-benzotrizol-1-yl)-1,1,3,3,-tetramethyl uroniumhexafluorophosphate) was used as the activating reagent without additionof supplemental benzotrizole. Dimethylformamide, piperidine andmethylene chloride (Baker) were fresh and stored under nitrogen.Anhydrous dimethylformamide was mixed with diisopropylethylamine (DIPEA,redistilled 0.46 M) to prepare the base activator solution.9-Fluorenylmethoxycarbonyl (F-moc)-protected amino acids utilized thefollowing side chain protecting groups: O-t-butyl (Asp, Glu); t-butyl(Tyr, Thr, Ser); 2,2,4,6,7-pentamethyldihydrobenzofuran-5-sulfonyl (Pbf)(Arg); t-butoxycarbonyl (Lys); and triphenylmethyl (Cys, His, Asn, Gln).Synthesis was performed on a 0.10 mmol scale using PAL (peptide amidelinker) resin (Fmoc-NH₂—CH₂-(di-m-methoxy,p-O-(CH₂)₄C(O)-polystyrene)which resulted in an amidated carboxy-terminus. Fmoc-amino acid and HATUwere used in four-fold excess (0.4 mmol per coupling). After the finalcoupling was completed, the Fmoc-protecting group was removed and theresin was washed for the last time. The resin was dried and stored in adesicator until cleavage and deprotection were initiated.

Reverse phase HPLC was performed using eluents composed of mixtures ofBuffer A (98% HPLC water, 2% acetonitrile, 0.05% trifluoroacetic acid)and Buffer B (20% HPLC water, 80% acetonitrile, 0.06% trifluoroaceticacid). All HPLC solvents were filtered through a 0.2 micron filter priorto use. Solvents and chemicals for peptide synthesis were obtained fromAldrich and Perseptive Biosearch unless stated otherwise. Peptides werelyophilized using a Savant SC100 Speed Vacuum instrument. Denaturingsodium dodecyl sulfate-polyacryalmide gel electrophoresis (SDS-PAGE)analysis was performed with a Pharmacia PhastGel system using HighDensity gels (20% acrylamide soaked in glycerol). Amino acid analysiswas assayed on a Beckman Analyzer.

For deprotection and purification of PPEBP1^(SH), PAL resin (15 mg)containing protected PPEBP1^(SH) was allowed to react for five hours atroom temperature in a deprotection cocktail (84% trifluoroacetic acid,4% phenol, 4% ethanedithiol, 4% thioanisole and 4% water). The solventwas removed by blowing a stream of nitrogen over the solution until thevolume reached approximately 0.25 ml. Diethylether (1 ml) anddithiothreitol (20 mg) were added to precipitate the peptide andstabilize the cysteine. The supernatant was removed after centrifugationand the precipitate dried. The crude peptide was dissolved in 1 mlphosphate-buffered saline (pH 7.5) with added dithiothreitol (5 mg) andfiltered with a 0.2 micron filter. The peptide was purified by reversephase HPLC (Vydac semipreparative 300 Å C18, 5 microns, 10.0×250 mm)using a 120 minute linear gradient of 100-30% Buffer A in Buffer B. Thepeptide eluted at 49.3 minutes using a flow rate of 4 ml/min and wasanalyzed by electrospray ionization mass spectrometry. The predicted andobserved masses were 4729.4 and 4730.0, respectively.

For preparation of PPEBP1^(SR), 0.080 mg of PPEBP1^(SH) was dissolved in0.50 ml of 2 mg/ml (15 mM) 2-bromoacetamide in 20 mM sodium phosphatebuffer (pH 7.5). The reaction was allowed to proceed for thirty minutesat room temperature. The peptide was purified by reverse phase HPLC(Rainin analytical 100 Å C18, 5 microns, 4.6×250 mm) using a fortyminute linear gradient of 100-30% Buffer A in Buffer B. The peptideeluted at 23.3 minutes using a flow rate of 1 ml/min and wascharacterized by electrospray ionization mass spectrometry and aminoacid analysis. AAA expected: Ala5 Asx5 CmCys1 Glx2 Phe1 Gly4 His0 Lle0Lys3 Leu2 Met0 Pro4 Arg8 Ser2 Thr1 Val2 Tyr2, found Ala5.2 Asx4.8CmCys0.6 Glx2.0 Phe1.0 Gly4.1 His0 Lle0 Lys2.9 Leu2.0 Met0 Pro3.7 Arg6.9Ser1.8 Thr0.8 Val2.0 Tyr1.8; mass predicted 4786.4, found 4787.1.

For deprotection and purification of PPEBP2^(SH), PAL resin (10 mg)containing protected PPEBP2^(SH) was allowed to react for seven hours atroom temperature in the deprotection cocktail and the solvent wasremoved. Diethylether (1 ml) and dithiothreitol (20 mg) were added, thesupernatant was removed after centrifugation and the precipitate dried.The crude peptide was dissolved in 1 ml phosphate-buffered saline (pH7.5) containing 5 mg fresh dithiothreitol and filtered. The peptide waspurified by reversed phase HPLC (Vydac semipreparative 300 Å C18, 5microns, 10.0×250 mm) using a linear 120 minute gradient of 100-50%Buffer A in Buffer B. The peptide eluted at 67.8 minutes using a flowrate of 4 ml/min and was characterized by electrospray ionization massspectrometry: mass predicted 4654.2, found 4653.6.

For preparation of PPEBP2^(SR), 0.070 mg of PPEBP2^(SH) was dissolved in0.50 ml of 2 mg/ml (15 mM) 2-bromoacetamide in 20 mM sodium phosphatebuffer (pH 7.5). The reaction was allowed to proceed forty minutes atroom temperature. The peptide was purified by reverse phase HPLC using afour minute linear gradient of 100-30% Buffer A in Buffer B (Raininanalytical 100 Å C18, 5 microns, 4.6×250 mm). PPEBP2^(SH) eluted at 24.9minutes using a flow rate of 1 ml/min, and was characterized byelectrospray ionization mass spectrometry and amino acid analysis. AAAexpected: Ala5 Asx6 CmCys1 Glx3 Phe1 Gly4 His0 Lie° Lys3 Leu2 Met0 Pro4Arg7 Ser2 Thr1 Val2 Tyr1, found Ala5.0 Asx5.8 CmCys0.9 Glx3.0 Phe1.0Gly4.0 His0 Lle3.0 Lys3.0 Leu2.1 Met0 Pro4 Arg7 Ser2 Thr1 Val2 Tyr1;mass predicted 4711.3, found 4710.8.

For deprotection and purification of EBP1^(SH), PAL resin (12 mg)containing protected EBP1^(SH) was allowed to react for six hours atroom temperature in the deprotection cocktail and treated as describedfor PPEBP1^(SR). The crude peptide was dissolved in 1 mlphosphate-buffered saline (pH 7.5) with added dithiothreitol (5 mg) andfiltered. The peptide was purified by reversed phase HPLC (Vydacsemipreparative 300 Å C18, 5 microns, 10.0×250 mm) using a 72 minutelinear gradient of 100-70% Buffer A in Buffer B. EBP1^(SH) eluted at49.6 minutes using a flow rate of 1 ml/min and was characterized byelectrospray ionization mass spectrometry: mass predicted 3346.9, found3346.2.

For preparation of EBP1^(SR), 150 micrograms of EBP1^(SH) was dissolvedin 0.50 ml of 2 mg/Ml (15 mM) 2-cromoacetamide in 20 mM sodium phosphatebuffer (pH 7.5). The reaction was allowed to proceed thirty minutes atroom temperature. The peptide was purified by reverse phase HPLC (Raininanalytical 100 Å C18, 5 microns, 4.6×250 mm) using a 40 minute lineargradient of 100-30% Buffer A in Buffer B. EBP1^(SR) eluted at 17.0minutes using a flow rate of 1 ml/min and was characterized byelectrospray ionization mass spectrometry and amino acid analysis. AAAexpected: Ala4 Asx3 CmCys1 Glx1 Phe1 Gly2 His0 Lie° Lys3 Leu2 Met0 Pro0Arg8 Ser1 Thr0 Val1 Tyr1, found Ala3.9 Asx3.0 CmCys0.9 Glx1.0 Phe1.0Gly2.1 His0 Lle0 Lys2.8 Leu2.0 Met0 Pro0 Arg6.9 Ser0.9 Thr0 Val1.0Tyr1.0; mass predicted 3404.0; found 3403.7.

For C/EBP₁₅₂, a stock solution of the purified C/EBP peptide wasprepared by dissolution in phosphate-buffered saline with 10 mMdithiothreitol. The solution was heated to 95° C. and allowed to slowlycool to room temperature in order to assure reduction of the cysteinenear the carboxy terminus of the peptide. The peptide was then usedimmediately for EMSA analysis. The peptide was characterized by aminoacid analysis. AAA expected: Ala8 Asx18 Glx18 Phe5 Gly6 His0 Lle4 Lys14Leu12 Met3 Pro6 Arg13 Ser15 Thr7 Val9 Tyr2, found Ala9.2 Asx16.9 Glx18.0Phe4.5 Gly7.0 His0 Lle3.8 Lys14.2 Leu11.3 Met2.7 Pro6.0 Arg10.8 Ser13.0Thr7.0 Val8.0 Tyr1.7.

Example 2 Binding of Miniature Proteins to DNA

Miniature protein-binding to DNA was measured using an electrophoreticmobility shift assay performed in a Model SE600 Dual-Controller VerticalSlab Unit (Hoefer) using 14×16 cm gel plates. Temperature was controlledusing a constant temperature bath. Reactions were performed in a bindingbuffer composed of 137 mM NaCl, 2.7 mM KCl, 4.3 mM Na₂HPO₄, 1.4 mMNaH₂PO₄ (pH 7.4), 1 mM EDTA, 0.1% NP-40, 0.4 mg/ml BSA (non-acetylated)and 5% glycerol. For experiments involving the bZIP peptide C/EBP₁₅₂,the binding buffer was supplemented with 2 mM dithiothreitol. Serialpeptide dilutions were performed as 1:1 dilutions with binding buffer.In general, 0.002 ml of gamma ³²P-labeled, double-stranded DNA (CRE₂₄,hsCRE₂₄, C/EBP₂₄ or hsCEBP₂₄; final concentration ≦50 pM in bindingbuffer; final concentration ≦5 pM for peptides with K_(app) <500 pM) inbinding buffer were added to 0.008 ml of a serial peptide dilution onice. Peptide-DNA mixtures were incubated for thirty minutes on ice andthen applied to a pre-equilibrated, native polyacrylamide gel (8%acrylamide:bisacrylamide) prepared in 10 mM Tris buffer (pH. 8.1). Gelswere allowed to run 0.75 to 1.5 hours at 500 V and were dried on a ModelSE1160 Drygel Sr. gel dryer (Hoefer). The gels were analyzed using aStorm 840 Phosphorimager (Molecular Dynamics). Amounts of free and boundDNA were quantified and analyzed using the program KaleidaGraph 3.0(Synergy Software). Dissociation constants were determined by fittingthe data to the Langmuir equation=c[(1+(K_(app)/peptide_(T) ^(n)))⁻¹]where n=1 for PPEBP^(SR) and EBP^(SR) and n=2 for C/EBP₁₅₂. In theseequations, theta=cpm in protein-DNA complex/(cpm in protein-DNAcomplex+cpm free DNA); peptide_(T)=the total peptide concentration and cis an adjustable parameter representing the maximum value of theta (c≦1; for many peptides c was defined as 1). Values reported represent theaverage of at least three independent trials ±the standard error. Errorbars on the plots represent the standard error for each data point.

For determination of binding stoichiometry, binding reactions wereperformed in the same buffer used for EMSA experiments. Each reactioncontained 200 nM hsCRE₂₄ and between 25 nM to 1600 nM PPEBP1^(SR). ThehsCEBP₂₄ concentration was determined by measuring the absorbance ofeach single stranded oligonucleotide at 260 nm. One strand of eachduplex was labeled with gamma-³²P. A small amount (0.010 ml) of labeledDNA was added to a 0.002 mM stock of the same strand. The ensure thatthe labeled strand annealed completely to its complement, an excess ofcold complementary strand was added and the mixture was allowed toanneal by heating to 95° C. for two minutes and slowly cooling to roomtemperature. Labeled hsCEBP₂₄ was added to the PPEBP1^(SR) solution andthe reaction incubated at 4° C. for thirty minutes before being appliedto a native 8% (80:1 acrylamide:bisacrylamide) prepared in 10 mM Trisbuffer (pH=8.0 at 4° C.). The gels were suspended in a chambercontaining 10 mM Tris buffer that was kept at 4° C. by immersion in awater-circulating temperature bath. The gels were dried and quantifiedwith a Phosphorimager (Molecular Dynamics).

No significant DNA binding was detected with peptides PPBRO^(SR) (SEQ IDNO: 8), PPBR10^(SR) (SEQ ID NO: 9) and PPBR11^(SR) (SEQ ID NO: 10) whichlacked one or more of these DNA-contact residues. High-affinity DNAbinding was observed with a peptide that contained these three residues:The equilibrium dissociation constant (K_(d)) of the PPBR2^(SR) (SEQ IDNO: 11) binding to hsCRE was 5 nM under conditions of physiologicalionic strength. DNA affinity was enhanced further by selective alaninesubstitutions that increased the overall alpha-helical propensity of thepeptide, producing the PPBR4^(SR)-hsCRE₂₄ complex whose K_(d) was 1.5 nMunder identical conditions. Formation of the PPBR4^(SR)-hsCRE₂₄ complexwas unaffected by high concentrations of poly (dIdC)-(dIdC) (Garner &Revzin, (1981) Nucl. Acids Res. 9, 3047-3048; Fried & Crothers, (1981)Nucl. Acids Res. 9, 6505-6506) or a scrambled CRE site (NON) indicatingthat the high stability of PPBR4^(SR)-hsCRE₂₄ was not due primarily tononspecific ionic interactions. Circular dichroism experiments indicatedthat like bZIP peptides (Weiss et al., (1990) Nature 347, 575-578;O'Neil, (1990) Science 249, 774-778), no detectable changes in secondarystructure occurred. PPBR4^(SR) (SEQ ID NO: 12) attained a fullyalpha-helical conformation only in the presence of specific DNA (The CDspectrum of PPBR4^(SR) was unchanged between 0.001 and 0.020 mM,indicating that no detectable changes in secondary structure occurred inthis range. Addition of hsCRE DNA significantly increased thealpha-helix content of PPBR4^(SR) while smaller changes were observedupon addition of hsCEBP DNA.

Although others have described monopartite DNA recognition by basicsegment peptides, the affinities reported have been only moderate (60nM-0.003 mM), and the complexes are stable only in very low ionicstrength buffers (Park et al., (1996) J. Am. Chem. Soc. 118, 4235-4239;Morii et al., (1996) J. Am. Chem. Soc. 118, 10011-10012). PPBR4^(SR)represents the first example of high affinity, monopartite, major grooverecognition at physiological ionic strength.

Example 3 Role of Hydrophobic Core in Miniature Protein-Binding to DNA

The contribution of hydrophobic core formation on PPBR4^(SR)-hsCRE₂₄complex stability was examined utilizing UV circular dichroismexperiments. Circular dichroism spectra were recorded in PBS on anAviv-202 CD spectrometer and were background corrected but not smoothed.Wavelength scans were performed at 4° C. between 200 and 260 nm at 1 nmintervals with a recording time of five seconds at each interval.Thermal denaturation curves were measured at 222 nm between 4° C. and98° C. with 2° C. steps and one minute equilibration at eachtemperature. Mean residue ellipticity and percent helicity werecalculated from the value at 222 nm after background correction.

G₂₇ lacked the polyproline helix and turn, whereas PPBR4-delta^(SR)contained D-tryptophan at position four and leucine at positionthirty-one. Modeling studies suggested that these substitutions woulddisrupt core formation by kinking the polyproline or the alpha-helix.The stability of the G₂₇-hsCRE₂₄ and PPBR4-delta^(SR)-hsCRE₂₄ complexeswere 3.1 and 3.2 kcal-mol⁻¹ lower, respectively, than that ofPPBR4^(SR)-hsCRE₂₄ complex. These data indicate that hydrophobic coreformation stabilized the PPBR4^(SR)-hsCRE₂₄ complex by as much as 3kcal·mol⁻¹.

Example 4 DNA Sequence Specificity of Miniature Protein Binding

The sequence specificity of PPBR4^(SR) was examined by comparing itsaffinity for hsCRE₂₄ (SEQ ID NO: 13) to that for hsCEBP₂₄ (SEQ ID NO:4), a sequence containing the half-site recognized by C/EBP bZIPproteins (Agre et al., (1989) Science 246, 922-926) using theelectrophoretic mobility shift assay described above. This half-site(ATTGC) differs from the CRE half-site (ATGAC) by two base pairs andprovides an excellent measure of base pair specificity (Suckow et al.,(1993) EMBO J. 12, 1193-1200; Johnson, (1993) Mol. Cell. Biol. 13,6919-6930). PPBR4^(SR) displayed remarkable specificity for hsCRE₂₄. Thespecificity ratio K_(rel) (K_(d)(hsCRE)/K_(d)(hsCEPB)) describingpreferred recognition of hsCRE₂₄ by PPBR4^(SR) was 2600 (delta,delta-G=−4.4 kcal·mol⁻¹). By contrast, G₅₆ which comprised the bZIPelement of GCN4, displayed low specificity. Specificity ratios of 118and 180 were observed for binding of CRE₂₄ (SEQ ID NO: 3) by G₅₆ inpreference to CEBP₂₄ (SEQ ID NO: 4) and hsCRE₂₄ in preference tohsCEBP₂₄ (delta, delta-G=−2.6 and -2.9 kcal·mol⁻¹, respectively). Therelative specificities of G₅₆ and PPBR4^(SR) were most recognizable whenone considered the concentration of each protein required to bindone-half of the two DNA. For PPBR4^(SR), this difference corresponded toa ratio of 2600, whereas for G₅₆, it corresponded to a ratio of eleven.PPBR4^(SR) more readily distinguished the two base pair differencebetween hsCRE₂₄ and hsCEBP₂₄ than G₅₆ distinguished CRE₂₄ from hsCEBP₂₄,two sequences that differed by six of ten base pairs. These comparisonsemphasize that PPBR4^(SR) was considerably more selective than was GCN4,the protein on which its design was based.

Example 5 Construction of Synthetic Genes Encoding a Miniature Protein

As described into detail below, the phage display vector pJC20 wasderived from the monovalent phage display vector pCANTAB5E (Pharmacia).pJC20 was prepared by inserting a synthetic gene encoding aPP betweenthe unique Sfi I and Not I restriction sites found in pCANTAB5E. Thesynthetic aPP gene contained codons for optimal protein expression in E.coli and four restriction sites (Xma I, Age I, Bgl II and Pst I) absentin pCANTAB5E. These restriction sites allow for the efficientconstruction of genes encoding a variety of discrete miniature proteinsas well as for the introduction of genetic diversity. The vector pJC21was prepared by inserting a synthetic gene encoding residues 18-42 ofPPBR4 between the unique Bgl II and Not I sites in pJC20. The identitiesof pJC20 and pJC21 were confirmed by automated DNA sequencing

A synthetic gene for aPP was constructed using codons chosen to optimizeexpression in E. coli and incorporated four unique restriction sites tofacilitate cassette mutagenesis. The 142 base pair duplex insert wasgenerated by use of mutually primed synthesis and the oligonucleotidesAPP.TS (CTA TGC GGC CCA GCC GGC CGG TCC GTC CCA GCC GAC CTA CCC GGG TGACGA CGC ACC GGT TGA AGA TCT GAT CCG TTT CTA CAA CGA CCT GCA GCA GTA CCTGAA CGT TGT TAC CCG TCA CCG TTA CGC GGC CGC AGG TGC G) (SEQ ID NO: 39)and APP.BS (CTA TGC GGC CCA GCC GGC CGG TCC GTC CCA GCC GAC CTA CCC CGGGTG ACG ACG CAC CGG TTG AAG ATC TGA TCC GTT TCT ACA ACG) (SEQ ID NO: 40)which overlap at nineteen base pairs. The reaction mixture (20 ml)contained 8 pmol APP.TS, 8 pmol APP.BS, 1× ThermoPol buffer (New EnglandBiolabs), 2 mg BSA, 1 mM dNTPs, 25 mCi [gamma-³²P] ATP, 5 mM MgSO₄ and 2ml Vent(exo-) DNA polymerase and was incubated at 94° C. for thirtyseconds, 60° C. for thirty seconds and 72° C. for one minute. The majorreaction product was purified from a denaturing (8 M urea) 10%acrylamide (29:1 acrylamide:bis-acrylamide) gel and amplified by PCR ina 0.100 ml volume containing 1,500 pmol of the primers CTA TGC GGC CCAGCC GGC CGG (SEQ ID NO: 41) and CGC ACC TGC GGC CGC GTA ACG (SEQ ID NO:42), 0.010 ml template, 0.25 mM dNTPs, 5 mM MgSO₄, 1× ThermoPol buffer(New England Biolabs) and 2 ml Vent(exo-) (New England Biolabs). The PCRreaction was subjected to thirty cycles of denaturation (94° C. forthirty seconds), annealing (60° C. for thirty seconds) and extension(72° C. for one minute). The insert was digested with Sfi I at 50° C. inNEB buffer two for four hours. This buffer was then supplemented withNaCl to a final concentration of 100 mM and with Tris-HCl to a finalconcentration of 50 mM before digestion with Not I for four hours at 37°C. The resulting insert was ligated into the vector pCANTAB-5E(Pharmacia) in a reaction containing 800 units T4 DNA ligase (NewEngland Biolabs), 50 mM Tris-HCl (pH 7.8), 10 mM MgCl₂, 10 mM DTT, 25mg/ml BSA, 1 mM ATP, 250 ng pCANTAB5E at 16° C. for one and a halfhours. The ligation products were transformed by electroporation intoTG1 E. coli and the resulting plasmid designated pJC20. A synthetic genefor PPBR4 was generated by replacing fifty-seven base pair at the 3′ endof the aPP synthetic gene (in pJC20) with the sequence encoding theC-terminal twenty-five amino acids of PPBR4.

The oligonucleotides PPBR4^(TS) (GAT CTG AAG CGC TTT CGT AAC ACC CTG GCTGCG CGC CGT TCC CGT GCA CGT AAA GCT GCA CGT GCT GCA GCT GGT GGT TGC GC)(SEQ ID NO: 43) and PPBR4^(BS) (CGC ACC TGC GGC CGC GCA ACC ACC AGC TGCAGC ACG TGC AGC TTT ACG TGC ACG GGA ACG GCG CGC AGC CAG GGT GTT ACG AAAGCG CTT CAG ATC TTC AAC C) (SEQ ID NO: 44) were annealed andphosphorylated on the 5′ end to form the PPBR4 insert. The PPBR4 insertwas ligated into pJC20 that had been previously digested with Bgl II andNot I and dephosphorylated with enzyme. The ligation reaction mixturecontained 800 units T4 DNA ligase in 50 mM Tris-HCl (pH 7.8), 10 mMMgCl₂, 10 mM DTT, 25 mg/ml BSA, 1 mM ATP, 90 ng digested pCANTAB-5E and8 ng annealed insert. After reaction, the ligation mixture wastransformed into electro-competent TG1 E. coli. The plasmid wasdesignated pJC21. The sequences of all final constructs were confirmedby automated sequencing.

Example 6 DNA-Binding Miniature Protein phage Library Construction

A 10 ml volume of 2xYT containing 100 mg/ml ampicillin and 2% glucosewas innoculated with a 500 ml overnight culture of TG-1 E. colicontaining the plasmids pJC20 or pJC21 and shaken at 37° C. to anOD₆₀₀=0.8. 4×10¹⁰ pfu of M13 KO7 helper phage were added and shakingcontinued for an additional one hour. Cells were pelleted for fifteenminutes at 5000×g and resuspended in an equal volume of 2xYT containing100 mg/ml ampicillin and 50 mg/ml kanamycin and grown for ten hours withshaking. Cells were pelleted by centrifugation at 5000×g for twentyminutes and the phage supernatant filtered through a 0.45 micron filterbefore precipitation with PEG/NaCl (20% w/v PEG-8000, 2.5 M NaCl inddH₂O) on ice for forty-five minutes. Phage were pelleted at 13000×g forthirty minutes at 4° C. and resuspended in binding buffer.

Example 7 Expression of Miniature Proteins by M13 Phage

As a first step towards displaying miniature proteins on the surface ofphage, the inventors sought to verify that aPP was expressed from thesynthetic gene, which is under the control of a lac promoter. To thisend, TG-1 E. coli harboring pJC20 were induced withisopropylthiogalactoside (IPTG), lysed and the cell lysates probed witha rabbit anti-aPP antibody (Peninsula Laboratories #RGG-7194) asdescribed below.

TG1 cells containing pJC20 were grown for one hour at 30° C. in 2xYTcontaining ampicillin at 100 mg/ml and 2% glucose. Cells were pelletedby centrifugation at 5000×g and resuspended in an equal volume of 2xYTcontaining 100 mg/ml ampicillin and 1 mM IPTG, grown for three hours at30° C. and then lysed by boiling in SDS sample buffer. Aliquots wereloaded onto a Pharmacia Phast HOMO 20 gel and electrphoresed at 95 Vuntil the solvent front ran off the gel. Proteins in the gel weretransferred to an Immobilon-P membrane at 65° C. for one hour. Themembrane was blocked for thirty minutes with TBST (20 mM Tris-HCl (pH8.0), 150 mM NaCl, 0.05% Tween-20) containing 0.5% BSA and thenincubated with a 1:10000 dilution of rabbit anti-aPP (PeninsulaLaboratories RGG-7194) provided at 4 mg/ml. The membrane was then washedthree times (five minutes per wash) with TBST and then incubated withTBST containing a goat anti-rabbit alkaline phosphatase conjugate (SantaCruz sc-2007) at a 1:1000 dilution. After three five minute washes withTBST and a single wash with TBS (TBST lacking Tween-20), the membranewas stained with VISTRA ECF (Pharmacia) and visualized at 405 nm on aSTORM 850 Phosphoimager (Molecular Dynamics).

For Western blots on phage particles, 10 ml of phage were produced andprecipitated with PEG/NaCl as described above. The phage were thenresuspended in 1 ml ddH₂O, precipitated with 200 ml of PEG/NaCl,resuspended in 100 ml ddH₂O and heated to 95° C. in SDS sample bufferfor ten minutes. The phage proteins were then applied to a 10% SDS gel(29:1 acrylamide:bisacrylamide) and subjected to electrophoresis at 20mA in Tris-glycine electrophoresis buffer until the solvent front ranoff the gel. The separated proteins were transferred to an Immobilon-Pmembrane (Millipore) at 20 V for four hours using a TE62 unit(Pharmacia) containing Towbin buffer (20% MeOH, 25 mM Tris-HCl (pH 8),192 mM glycine, 0.1% SDS (w/v)) at 4° C. After blocking with 5% nonfatmilk in TBST for sixteen hours and washing twice (five minutes per wash)with TBST, the membrane was probed for thirty minutes with anti-aPP inTBST supplemented with 2.5% nonfat milk. The membrane was washed threetimes (five minutes per wash) with TBST, then exposed to a goatanti-rabbit antibody-alkaline phosphatase conjugate (Santa Cruz sc-2007)at a 1:5000 dilution in TBST supplemented with 2.5% nonfat milk forfifteen minutes. After washing three times (five minutes per wash) withTBST and two times (five minutes per wash) with TBS the membrane wasstained with VISTRA ECF (Pharmacia) and visualized at 405 nm on a STORM850 phosphorimager (Molecular Dynamics).

These experiments demonstrate clear evidence for IPTG-inducibleexpression of aPP fused to the minor capsid protein III of M13bacteriophage. To investigate whether this fusion protein was assembledinto viable phage particles, purified phage were, phage proteinsresolved using SDS-PAGE and probed with the rabbit anti-aPP antibody.The Western blot clearly shows that the fusion protein containing aPPand protein III is incorporated into fully assembled M13 phageparticles. No signal was observed when phage produced from pJC21 bearingcells were probed with the rabbit anti-aPP antibody

Example 8 Functional Selection of DNA-Binding Miniature Proteins onPhage

As a first step towards the optimization of PPBR4, the inventorsconfirmed that phage displaying PPBR4 could be selected over phagebearing aPP when sorted on the basis of specific DNA-binding. Phagedisplaying either PPBR4 or its progenitor aPP were panned againstmagnetic beads coated with a twenty-four base pair duplexoligonucleotide containing the five base pair sequence recognized byPPBR4, half site CRE (hsCRE, ATGAC). The DNA was attached tostreptavidin coated beads through a 3′ biotin TEG (triethyleneglycol)linker (Glen Research). Panning was performed essentially as previouslydescribed and as set forth below (Choo & Klug, (1994) Proc. Natl. Acad.Sci. USA 91, 11163-11167).

For panning experiments, 0.5 mg of streptavidin-coated M-280 magneticbeads (Dynal) were washed six times with 50 ml of 2×B+W buffer (10 mMTris-HCl (pH 7.5), 1 mM EDTA, 2.0 M NaCl). Each wash step was performedfor two minutes. The beads were blocked by incubation in 50 ml of 1×B+Wcontaining 6% nonfat milk for fourteen hours. The beads were then washedfive times with 50 ml of 1×B+W and resuspended in 50 ml of 1×B+Wcontaining approximately 1 mM duplex hsCRE242 carrying a 3′ biotin labelon one strand for twelve minutes. This procedure loaded approximately 75pmol DNA per mg bead. The beads were then washed five times with 50 mlof phage binding buffer (phosphate buffered saline supplemented with 0.4mg/ml BSA, 0.1% NP-40 and 2.5 mg of poly-dIdC). 1010 phage in a volumeof 0.4 ml were added to the beads at 4° C. and incubated with rotationon a Labquake shaker rotisserie for two hours. Beads were washed fivetimes for five minutes at 4° C. with wash buffer (phage binding bufferlacking poly-dIdC). Bound phage were eluted by the addition of washbuffer containing 4 M NaCl and an increase in temperature to 25° C. fortwo hours. 200 ml of the elution and 200 ml of phage not subject topanning were used to infect 7 ml of log phase TG-1 E. coli. After onehour, serial dilutions of infected cells were plated on SOBAG (SOB mediasupplemented with ampicillin to 100 mg/ml and 2% glucose) and grown fortwelve hours at 30° C. Values of percent retention were calculated wherepercent retention=(output titer/input titer)×100.

In the present experiments, wash conditions were optimized to maximizedifferential retention of phage displaying PPBR4 and phage displayingaPP. In phosphate buffered saline (PBS) supplemented with 0.1% NP-40,0.4 mg/ml BSA and 2.5 pg/ml poly-dIdC, the percent retention of PPBR4phage on hsCRE beads was ten times greater than that of aPP phage. Thisresult indicates that miniature proteins generated by protein graftingcan be functionally selected on M13 phage.

Example 9 Isolation of Highly Selective DNA-Binding Miniature Proteins

Two phage libraries were created essentially as described in theprevious examples to identify appropriately folded PPBR4 analogs thatwould bind with higher affinity and specificity. The members oflibraries A and B differ from PPBR4 at three (library A) or four(library B) positions on the PPII helix. The proline residues retainedat positions two and five of library A are highly conserved amongPP-fold proteins. It was anticipated that retention of these twoprolines would effectively constrain the conformational space availableto library A members and that most would contain N-terminal PPIIhelices. Such conformational constraints are absent in library B,acknowledging that there may be many ways to stabilize DNA-boundalpha-helices.

Since the amino acids at positions two and five of library B are notrestricted to proline, it was anticipated that this library would samplea larger fraction of available phi-psi space. Phage were sorted forthree rounds on the basis of their ability to bind an oligonucleotideduplex containing the sequence ATGAC (hsCRE). To favor identification ofsequences that bound hsCRE with high affinity at ambient temperature,two rounds of selection at 4° C. were followed by a single round at roomtemperature. By the final round, library A phage were retained at alevel only comparable to PPBR4 phage and were not considered further.Library B phage were retained at a level comparable to PPBR4 phage afterthe first round, but at levels fifteen to sixteen times better thanPPBR4 phage after the subsequent two rounds. Twelve library B cloneswere sequenced after round three. Six sequences (p007, p009, p011, p012,p013, and p016) were synthesized and the DNA-binding properties of fouranalyzed in detail.

Quantitative electrophoretic mobility shift experiments were performedas described in the previous examples to assess the DNA affinities ofp007, p011, p012, and p016. All peptides tested bound hsCRE as well orbetter than did PPBR4 or G₂₇ (the isolated basic region of GCN4). At 4°C., p011 and p012 bound hsCRE with affinities of 1.5±0.2 nM and 2.5±0.5nM, whereas p016 bound hsCRE with an affinity of 300±60 pM. Ofparticular interest is p007, which bound hsCRE to form an exceptionallystable complex with a dissociation constant of 23±1.2 μM. This peptidebound specific DNA approximately 100-times better than did PPBR4(K_(d)=1.9±0.2 nM) and approximately 20,000 times better than did G₂₇(K_(d)=410±53 nM). Moreover, at 25° C. p007 bound hsCRE with an affinityof 1.6±0.1 nM. Neither PPBR4 nor G₂₇ showed evidence of DNA binding atthis temperature. P007 binds specific DNA considerably more tightly thantwo fingers from the Tramtrack zinc finger protein, which binds fivebase pairs of DNA with an affinity of 400 nM (Segal & Barbas, (2000)Curr. Op. Chem. Biol. 4, 34-35).

Example 10 Specificity of Highly Selective Miniature Protein DNA-Binding

The specificity of DNA binding was investigated by determining theaffinity of p007 for several duplex oligonucleotides containing two basepair changes within the five base pair hsCRE sequence using quantitativeelectrophoretic mobility shift assays as described in the previousexamples. p007 was extremely discriminating, exhibiting a specificityratio R (defined as the ratio of the dissociation constants of specificand mutated complexes) between 200 and 800 (delta, delta-G=−3.3 to 4.0kcal mol⁻¹). This high level of discrimination was observed across theentire five base pair hsCRE sequence, indicating that no singleinteraction dominated the free energy of the p007-hsCRE complex and thatthe binding energy is partitioned across the entire protein-DNAinterface. By contrast, at 4° C. PPBR4 discriminates poorly (delta,delta-G=−1.7 kcal mol⁻¹) against sequences possessing mutations at the5′ terminus of hsCRE.

To investigate the possibility that DNA sequences other than these fourmight bind p007 tightly, the affinity of p007 for calf thymus DNA (CTDNA) which possesses a potential binding site in every register oneither DNA strand was measured. The average specificity ratio forrecognition of hsCRE in preference to any site in CT DNA was 4169. Thisratio is considerably greater than the number of potential competitorsites (4⁵=1024). Whereas the triple zinc finger construct Zif268 andvariants thereof selected by phage display fail to uniquely specify oneto two base pairs of their nine base pair binding sites (Li et al.,(1992) Biochemistry 31, 1245-1253), p007 completely specifies all fivebase pairs of its target sequence. In fact, even if each possible fivebase pair competitor site were present at equal molarity to the targetsite, 80% of the p007 molecules would be bound to hsCRE, despite theeffects of mass action.

Example 11 NMR Characterization of Miniature Protein Structure

For NMR Spectroscopy, p007 was dissolved in 90% H₂O/10% D₂O containing 4mM KCl, 205 mM NaCl, 6.5 mM Na₂HPO₄, 2.1 mM KH₂PO₄ (pH 7.4). Peptideconcentration was approximately 1.5 mM. Chemical shifts were referencedin ppm from internal 3-(trimethylsilyl)propionic-2,2,3,3-d4 acid, sodiumsalt. All spectra were recorded on a Varian 800 MHz Inova instrument at2° C. with a sweep width of 9000 Hz. NOESY experiments were performedusing a waterflip-watergate pulse sequence for water suppression with4096t2×500t1 complex points. Mixing times of 50, 150 and 300 ms wereacquired. DQF-COSY spectra (60 ms mixing time) were acquired with2048t2×300t1 complex points. Data was processing was performed on aSilicon Graphics Workstation using Felix 98 (MSI). Prior to Fouriertransform of the free induction decays, a gaussian window function wasapplied to NOESY spectra, while a Kaiser window function was applied toDQF-COSY spectra. The digital resolution of the NOESY spectra was 2.2Hz/pt. DQF COSY data was zero filled to yield a 8192×8192 matrix with adigital resolution of 1.1 Hz. Spectra were assigned by standard methods.

Multidimensional NMR experiments allowed for characterization of thestructure of p007 in greater detail. The backbone and side-chainconnectivities in p007 were assigned on the basis of reasonably disperseNOESY spectra. The presence of amide-amide cross peaks between residuesat positions i and i+3 and i and i+4 defined an alpha-helicalconformation for residues 14-30. Eleven long range NOEs between residues8 and 17, 8 and 20, 7 and 20, 5 and 20, 4 and 27, 2 and 29, 2 and 30specify a folded structure that superimposes on residues 5-8 and 15-28of aPP with a backbone rmsd of 1.6 A. Thus, the main chain folds of p007and aPP are remarkably similar, with residues 5, 7 and 8 proximal toresidue 20 and residues 1 and 2 proximal to residue 30. As in previousstudies of pancreatic fold polypeptides (Blundell et al., (1981) 78,4175-4176), the PPII helix proposed for residues 1-8 of p007 isunder-defined by the NMR data. However, in light of the similaritybetween the aPP and p007 folds, p007 must contain a structure similar toa PPII helix.

Example 12 Protein-Binding Miniature Protein Phage Library Construction

For construction of the aPPBAK library, mutagenesis was carried outusing the NNS codon scheme, where N=any base and S=G/C. This schemecodes for all twenty amino acids and the amber stop codon TAG which issuppressed by insertion of glutamine in the E. coli SupE strains used.The oligonucleotides BAKLIB: GGT GAC GACGCA CCG GTT GAA GAT CTG ATC CGCTTT GTT NNS CGT CTG CTG NNS TAC ATC NNS GAC NNS ATC AAC CGT CGT GCG GCCGCA GGT GCG (SEQ ID NO: 45) and PBAKLIB: CGC ACC TGC GGC GGCACG ACG (SEQID NO: 46) were synthesized and purified by denaturing gelelectrophoresis. 400 pmol of each oligonucleotide were annealed in 1×Sequenase buffer (USB) in a total volume of 0.20 ml. The annealedoligonucleotides were converted to duplex DNA by primer extension uponaddition of 2.5 mM dNTPs, 1 mg/ml BSA and 50 units Sequenase (USB) andincubation at 37° C. for thirty minutes. The duplex DNA was digested in1× buffer 3 (New England Biolabs) by the addition of 0.015 ml Bgl II,0.015 ml Not I, 2.5 mM DTT, 0.1 mg/ml BSA in a total volume of 0.430 ml.The reaction mixture was extracted twice with an equal volume of Trisbuffered phenol (pH 8.0) and applied to a 15% acrylamide (29:1acrylamide:bisacrylamide) gel in 1×TBE at 500 V. The doubly digestedproduct was visualized by ethidium staining, excised and extracted in1×TE. The insert was ethanol precipitated. 0.12 mg of the vector pJC20was digested with 0.05 ml of Bgl II, Not I and Pst I in a total volumeof 0.60 ml. The digested vector was purified by Chromaspin 1000 sizeexclusion chromatography (Clonetech) and phenol chloroform extractionfollowed by ethanol precipitation. Ligations were performed using theLigation express kit (Clontech) with 830 ng of vector (pJC20) and 14 ngof insert. Transformation by electroporation in to TG-1 E. coli yielded3×10⁶ transformants. The number of transformants is greater than thetheoretical diversity of the library (32⁴=1.05×10⁶) and the library isstatistically greater than 90% complete. Automated DNA sequencing oftwenty clones showed the mutant genes were inserted correctly in allcases.

Example 13 Functional Selection of Protein-Binding Miniature Proteins onPhage

For biopanning of the aPPBAK library, a glutathione coated microtiterplate (Reacti-bind glutathione coated plate #15140, Pierce) was washedthree times with 0.20 ml of PBS per wash. Human recombinant Bcl-2(1-205) was obtained as a soluble GST-fusion from Santa CruzBiotechnology. 9.0 pmol of Bcl-2 in 0.20 ml of PBS was added to eachwell and incubated at 4° C. for twelve hours with shaking. The wellswere then blocked for three hours with 0.20 ml of TBST containing 5%nonfat dry milk. Before use, the well was washed three times with TBSTfor five minutes per wash.

Phage were produced, harvested and propagated as described in theprevious examples, with the exception that, in rounds three throughfive, XL1-blue cells were used instead of TG-1 cells to propagate phageparticles. This change eliminated problems encountered previously withdeletions in later rounds of selection, which are attributed to the RecA+nature of TG-1 E. coli. Phage particles were resuspended in 2 ml ofTBST. 0.20 ml of phage (1×10¹⁰ particles) were added to each well andincubated for three hours at 4° C. in the first two rounds of selectionand at 25° C. in the final three rounds. The wells were then washed tentimes with 0.20 ml of TBST, two minute washes in the first round andfive minute washes in subsequent rounds. Washes were performed at thesame temperature in the binding reaction. After five rounds ofselection, sixteen clones were sequenced by automated DNA sequencing.

The phage library BAKLIB was subjected to five rounds of panning againstimmobilized GST-Bcl-2. The percent retention of the phage libraryincreased 225-fold over the course of the selection from 0.01% in thefirst round to 2.25% in the fifth round. This increase in retentionunderestimates the improvement of library retention because the finalround was carried out at 25° C. while the first round was performed at4° C. After five rounds sixteen phagemid library clones were sequenced.The selected sequences (FIG. 1) show a high degree of convergence. Sevendistinct sequences were isolated with four sequences representedmultiple times. Interestingly, residue 28 in the library, whichcorresponds to I₈₁ of Bak, is mutated to F in eleven of sixteen roundfive clones, although it was fixed in the initial pool. This resultindicates that within the context of the scaffold, F₂₈ is better atbinding into the hydrophobic pocket of Bcl-2 than I₂₈. Eleven of sixteensequences contain glycine at positions 75 and 82 as in Bak. Indeed, onesequence that was represented two of sixteen times contained residuesidentical to those of Bak at all four randomized positions, thissequence however, also contained the I-F mutation at position 28.Comparison of the selected sequences to other BH3-containing proteinsreveals further similarities. For example, at position 26 of thelibrary, R occurred in seven of the sixteen sequences and R or K is thepreferred amino acid at this position (residue 79 in Bak) in most BH3domains. Similarly, an E at position 31 of the library was selected insix of sixteen sequences, where E/D is the preferred amino acid at thecorresponding position of most known BH3 domains.

The similarities of selected amino acids at these positions to those inBak and other BH3 domains indicates that the sequences of BH3 domainsarose from the requirement to bind Bcl-2 family proteins and not forother biological function. Further, it also indicates that the selectedpeptides bind Bcl-2 in the same hydrophobic pocket as does Bak.Interestingly, one sequence represented twice contained a threonine atposition 31 of the library. This residue provides both the methyl groupof a valine which could contribute to hydrophobic core formation and ahydroxyl group that could provide a hydrogen bond acceptor like thenative D/E residue in BH3 domains. One sequence that appeared twice inthe round five clones sequenced contained a single amino acid deletionwith respect to the library design that places both the aPP foldingresidues and the Bcl-2 residues out of register.

Example 14 Synthesis of Protein-Binding Miniature Proteins

Peptides were synthesized on a 0.10 mM scale using Fmoc chemistry. Eachpeptide contained a free N-terminal amine and a C-terminal amide.Peptides were purified by reverse phase HPLC as described in theprevious examples. Two sets of peptides were prepared, peptides4099-4102 and the Bak peptide (SEQ ID NO: 73). Peptides for fluorescentlabeling and subsequence IQ determinations contained an additionalcarboxy-terminal YC sequence (the Y is derived from the native sequenceof Bak), the cysteine of which was labeled with5-iodoacetamidofluorescein (51AF). Peptides at a final concentration of200-400 mM were alkylated on the sulfur atom of C-terminal cysteines byincubation with ten equivalents of 51AF (Molecular Probes) in 0.20 ml ofa 50/50 mixture of DMF and PBS. The labeling reaction was performed inthe dark for six hours at room temperature. Alkylation was essentiallyquantitative as judged by HPLC. Labeled peptides were purified byreverse phase C-18 HPLC. The identifies of the peptides were verified byMALDI-TOF mass spectrometry (Voyager, Perseptive Biosystems). Themolecular weights were as expected: p4099 theoretical [MH+]=3907,observed [MH+]=3907; p4100 theoretical [MH+]=4020, observed [MH+]=4020;p4101 theoretical [MH+]=3921, observed [MH+]=3922; p4102 theoretical[MH+]=3901, observed [MH+]=3902; Bak 72-94 theoretical [MH+]=1724,observed [MH+]=1723; p4121-flu theoretical [MH+]=4562, observed[MH+]=4560; p4122 theoretical [MH+]=4675, observed [MH+]=4766; p4123theoretical [MH+]=4576, observed [MH+]=4577; p4124 theoretical[MH+]=4556, observed [MH+]=4556; Bak-flu theoretical [MH+]=2535,observed [MH+]=2535. Peptide concentrations were determined by aminoacid analysis.

Example 15 Binding of Miniature Proteins to Other Proteins

To measure the equilibrium dissociation constant of Bcl-2 binding to theselected peptides or the Bak BH3 peptide, Bcl-2 was serially dilutedfrom 0.0036 mM in PBS with the fluorescently labeled peptide added at aconstant concentration between 0.020-0.040 mM. After equilibration forforty minutes at 4° C., the fluorescein was excited at 492 nm using aPS-220B lamp power supply (Photon Technologies) and the fluorescenceemission spectra between 505 and 560 nm recorded on an 814photomultiplier detection system (Photon Technologies) with a 2 nmstepsize and a one second equilibration time, using 5 nm slit widths.The fluorescence emission maxima at 515 nm for three independent trialswere averaged and the dissociation constants calculated as previouslydescribed. Similar experiments were used to determine the dissociationconstants for the Bak peptide or selected peptides binding carbonicanhydrase II (Sigma) or calmodulin (Sigma). The calmodulin binding wasmeasured in a buffer composed of 20 nM HEPES (pH. 7.2), 130 mM KCl, 1 mMCaCl₂ while carbonic anhydrase binding was measured in PBS.

The Bak peptide along with four sequences represented multiple times inthe sixteen sequenced clones from round five were chemicallysynthesized. Bcl-2 binding affinity of the peptides was determined bymeasuring the change in fluorescence emission of a carboxy-terminalfluorescein label on the peptide as a function of Bcl-2 concentration.To validate this assay the K_(d) for the Bak peptide binding to Bcl-2was measured. This K_(d) was 363 nM±56 nM, consistent with a K_(d) of340 nM previously reported for the Bak peptide Bcl-X_(L) interaction(measured by fluorescence quenching of intrinsic tryptophan inBcl-X_(L)) and a K_(d) of about 200 nM reported for the Bak Bcl-2interaction (measured by fluorescence polarization of a fluoresceinlabeled Bak peptide). The K_(d) for the selected peptides were: p4099K_(d)=352±33 nM, p4100 K_(d)=401±40 nM, p4101 K_(d)=811±20 nM, p41023700±1400 nM. The K_(d) for all the peptides without deletions indicatethat they bind significantly better than the mutant p4102 that containsa deletion in the alpha-helix. Within this series of peptides, p4099(GAGT) binds about two-fold better than p4101 (GAGD), that differs inonly a D to T mutation at position 31. p4100 (GRGE) binds withcomparable affinity to p4099 indicating that these two peptidesrepresent convergent and equal solutions to forming a protein-proteininterface.

In order to compare the specificity of 4099 to the Bak peptide, theirinteraction with Calmodulin was investigated. Calmodulin is known tobind a range of alpha helices and Carbonic anhydrase II, which has alarge hydrophobic cavity. p4099 bound Calmodulin with a K_(d) of0.025±0.004 mM, while the Bak peptide bound Calmodulin with a K_(d) of0.025±0.004 mM. p4099 bound Carbonic anhydrase II with a K_(d) of0.0086±0 mM, the Bak peptide bound Carbonic anhydrase with a K_(d) of0.022±0.0046 mM. p4099 discriminates well against these non-specificproteins indicating that the interaction between the peptide and Bcl-2results from a stereospecific set of VanderWaals contacts.

Example 16 Structure of Protein-Binding Miniature Proteins

Circular dichroism spectra were recorded in PBS on an Aviv 202 CDSpectrometer and were background corrected but not smoothed. Wavelengthscans were performed at 4° C. between 200 and 260 nm at 1 nm intervalswith a recording time of five seconds at each interval. Bak (72-94),4099, 4100, 4101, 4102 were used at concentrations of 0.028 mM, 0.0069mM, 0.0119 mM, 0.014 mM and 0.016 mM respectively. Thermal denaturationcurves were measured at 222 nm between 4-98° C. with 2° C. steps and oneminute equilibration at each temperature. Peptides were used at thehighest concentrations used for the wavelength scans described above.Mean residue elliptcity and percent helicity were calculated from thevalue at 222 nm after background correction.

The structure of peptides was investigated by far UV circular dichroismas described above. Wavelength scans reveal the previously reportedrandom coil signature for the Bak peptide. In contrast the selectedpeptides 4099, 4100, 4101, 4102 show minima at 208 and 222 nm,characteristic of alpha-helical content. The mean ellipticity of peptide4099 was shown to be concentration independent down to the lowestconcentration measurable 0.0011 mM. The percentage helicity of p4099 isapproximately 60%, consistent with an aPP-like tertiary fold in whichresidues 14-35 adopt a helical confirmation. This helicity is comparableto that seen for p007, a peptide evolved to bind DNA with high affinityand specificity as described in the previous examples. Thermaldenaturation of the peptides was monitored by far UV circular dichroismat 222 nm. p4099 had a cooperative thermal melt with a T_(m) ofapproximately 65° C., comparable to the T_(m) reported for aPP.

Example 17 Miniature proteins for inhibiting MDM2-p53 interactions

MDM2 is the principal cellular antagonist of the tumor suppressorprotein p53 (Wu et al., J. Genes Dev. 1993, 7, 1126). MDM2 antagonizesp53 function by sequestering the p53 transcriptional activation domainand targeting it for ubiquitin-dependent degradation by the 26Sproteasome. Elevated MDM2 levels are found in a variety of solid tumorscontaining wild type p53 and there is considerable interest in MDM2ligands capable of up-regulating p53 activity in vitro or in vivo. Thehigh-resolution structure of the MDM2·p53 activation domain peptide(p53AD) complex reveals an irregular p53AD α-helix nestled into a deep,hydrophobic, MDM2 cleft (Kussie, et al., Science 1996, 274, 948). Thisstructure, along with accompanying mutagenesis data, suggests thatcomplex stability (K_(d)=600 nM) derives predominantly from interactionsbetween three p53AD residues (F19, W23, and L26) and several residueslining the MDM2 cleft.

Residue-by-residue alignment of the α-helical segments of p53 and aPP(FIG. 2B) positions the three critical MDM2 contact residues (F19, W23,and L26) and the five important aPP folding residues (L14, F17, L21,Y24, L25) on the solvent-exposed and solvent-sequestered faces,respectively, of the aPP α-helix. Five remaining α-helical residues werevaried across all twenty amino acids to (1) foster additionalinteractions with MDM2; (2) sustain the aPP fold; and (3) acknowledgethe imperfect phi and psi angles found within p53AD bound to MDM2(Kussie, et al., Science 1996, 274, 948). The M13 phage library preparedcontained 6×10⁷ unique transformants, insuring that it would evaluateDNA sequence space with >83% confidence. Three rounds of selection forbinding GST-MDM21 immobilized on glutathione-coated microtiter plates2led to a 100-fold enrichment in affinity. Several peptides from rounds 2and 3 (FIG. 2B) were synthesized with a cysteine residue at theC-terminus and labeled with 5-iodoacetamidofluorescein to facilitatefluorescence polarization analysis of MDM2 affinity (all syntheticpeptides were purified to homogeneity by HPLC and characterized byMALDI-TOF mass spectrometry and amino acid analysis).

Fluorescence polarization analysis indicated that all selected miniatureproteins bound GST-MDM2 in the nanomolar concentration range (FIG. 3).pP53-05, in particular, bound GST-MDM2 to form a complex with anequilibrium dissociation constant (K_(d)) of 99±11 nM, a value that issignificantly more favorable than that of the p53AD·MDM2 complex(K_(d)=261±59 nM) (Kussie, et al., Science 1996, 274, 948). ThuspP53-05, which contains only 31 residues, binds MDM2 as well or betterthan 109 residue thioredoxin derivatives that present p53AD (andvariants thereof) on an active site loop (Bottger, et al., J. Med. Chem.2000, 43, 3205). The CD spectrum of pP53-05 (2.75 μM) was characterizedby negative ellipticity at 208 and 222 nm that was comparable to that ofaPP and underwent a cooperative melting transition (T_(m)) at 47° C.(FIG. 4).

The specificity of pP53-05 was evaluated by measuring its affinity forseveral receptors and enzymes that bind helical or hydrophobic peptidesor small molecules (FIG. 3). Calmodulin, an EF hand protein known forits ability to bind many α-helical peptides and proteins (Meador, etal., Science 1991, 257, 1251), bound pP53-05 in the high micromolarconcentration range (K_(d)>275 μM). Similar K_(d) values characterizedthe affinity of pP53-05 for the bZIP region of Fos, which forms dimericcomplexes with other bZIP proteins (42 μM) (Glover, et al., Nature 1995,373, 257), for carbonic anhydrase, which binds CO₂ (298 μM) (Liljas, etal., Nat. New Biol. 1972, 235,131), and for protein kinase A, whichbinds the α-helical peptide inhibitor pKI (16 μM) (Knighton, et al.,Science 1991, 253, 414). The large difference (ΔΔG=2.8-4.4 kcal·mol⁻¹)between the stabilities of these complexes and that of pP53-05·GST-MDM2suggests that the latter is stabilized by highly stereospecific van derWaals interactions whose energetic benefit exceeds that availablethrough non-specific protein contacts.

To establish whether pP53-05 bound MDM2 in a manner that would inhibitbinding of p53AD, we incubated GST-MDM2 and p53AD-Flu with varyingconcentrations of pP53-05 and monitored the fraction of p53AD-Flu boundat equilibrium (FIG. 3). In the absence of pP53-05, 60% of p53AD-Flu isbound to GST-MDM2 under these conditions. Addition of pP53-05 led to aconcentration-dependent decrease (K₁=722 nM) in the fraction ofp53AD-Flu bound to GST-MDM2. Similar K_(i) values were determined atshorter and longer incubation times, confirming that equilibrium hadbeen reached. By comparison, competition of p53AD-Flu by unlabeled p53ADwas characterized by K_(i)=1.2 μM.

In conclusion, we have shown that protein grafting, in combination withfunctional selection, provides rapid access to miniature protein ligandsfor globular protein surfaces. The molecules we describe possessaffinities in the nanomolar concentration range and effectivelydiscriminate against other proteins, even those that bindnon-selectively to other helical, hydrophobic proteins. The combinedfeatures of high affinity, high selectivity and a compact protein foldshould enhance the utility of miniature proteins for a wide variety ofbioengineering and proteomics applications (Zhang, et al., Nat. Biotech.2000, 18, 71).

Example 18 Miniature Proteins for Inhibiting Protein Kinase A

The design of selective protein kinase inhibitors remains a significantchallenge (Bridges, et al., J. Chem Rev 2001, 101, 2541-72; Scapin, etal., Drug Discov Today 2002, 7, 601-11) because of both sheer numbers(more than 500 different kinases are found in a mammalian cell) and thehighly conserved nature of the ATP binding site

(Miller, W. T. Nat Struct Biol 2001, 8, 16-8). Only a small number ofselective kinase inhibitors are known (Bridges, et al., J. Chem Rev2001, 101, 2541-72; Cohen, et al., Curr Opin Chem Biol 1999, 3, 459-65;Zimmermann, et al., Bioorg Med Chem Lett 1997, 7, 187-92).

The indolocarbazole natural product K252a is a potent, active-sitedirected inhibitor of many tyrosine and serine/threonine kinases and acommon starting point for the discovery of specific kinase inhibitors(Kase, et al., J Antibiot 1986, 39, 1059-65; Kase, et al., BiochemBiophys Res Commun 1987, 142, 436-40; Hashimoto, et al., Biochem BiophysRes Comm 1991, 181, 423-9; Tapley, et al., Oncogene 1992, 7, 371-81). Wehave described a miniature protein design strategy in which thewell-folded helix in avian pancreatic polypeptide (aPP) presents shortα-helical recognition epitopes. The miniature proteins designed in thismanner recognize even shallow clefts on protein surfaces with nanomolaraffinities and high specificity (see, e.g., Examples 19-20). Here wedemonstrate that designed variants of aPP can also impose specificity onthe potent but otherwise non-selective kinase inhibitor K252a byrecognizing non-conserved features of the protein surface surroundingthe ATP binding pocket. Our results suggest that bifunctional moleculesthat embody elements of protein surface recognition could represent aviable general strategy for selective kinase inhibition.

Our design began with the structure of the catalytic subunit ofcAMP-dependent protein kinase (PICA) in complex with PKI₅₋₂₄, a peptiderepresenting the active portion of the heat-stable Protein KinaseInhibitor protein (Glass et al., J Biol Chem 1989, 264, 8802-10;

Zheng, et al., Acta Cryst 1993, D49, 362-5) (FIG. 5). In this complex,the PKI₅₋₂₄C-terminal pseudosubstrate (residues 17-24) occupies thepeptide substrate-binding site with energetically significant contactsfrom R18, R19, and 122 and R15 from the adjacent turn (residues 15-16);the N-terminal alpha helix (residues 5-13) nestles in a shallowhydrophobic groove outside the substrate-binding site with anenergetically significant contact from F10. Two separate alignments ofthe sequences of the aPP and PKI₅₋₂₄ α-helices were considered (FIG. 6).Both alignments retain F10 of the PKI₅₋₂₄α-helix, all threepseudosubstrate contacts, and all residues required to maintain the aPPfold; alignment #1 also retains R15. The resulting molecules, 1 and 2,were synthesized using standard solid phase methodology. A cysteineresidue added to the C-terminus was modified with5-iodo-acetamidofluorescein to facilitate fluorescence polarizationanalysis of PKA affinity.

The relative affinities of 1^(Flu), 2^(Flu) and PKI₅₋₂₄ ^(Flu) for thecatalytic subunit of PKA were measured by fluorescence polarizationanalysis in the presence and absence of ATP (FIG. 7). In the presence of100 μM ATP, the complex between PKA and 1^(Flu) was characterized by anequilibrium dissociation constant (K_(d)) of 99±39 nM (FIG. 7 a). Thestability of PKA·1^(Flu) was only 3-fold lower than that of PKA·PKI₅₋₂₄^(Flu) under identical conditions (K_(d)=31±8 nM). 2^(Flu) bound PKAwith much lower affinity (K_(d)=570±123 nM), perhaps because it lackedR15, and was not considered further. Surprisingly, 1^(Flu) retainedsignificant affinity for PKA in the absence of ATP (K_(d)=230±34 nM)(FIG. 7 b). By contrast, PKI₅₋₂₄ ^(Flu) bound PKA far more poorly in theabsence of ATP, as expected (Whitehouse, et al., J Biol Chem 1983, 258,3693-701), showing a 50-fold decrease in affinity (K_(d)=1.6±0.4 μM).Previous structural and biochemical studies have documented the dramaticchange in PKA conformation induced by the binding of ATP (Johnson, etal., Chem Rev 2001, 101, 2243-70). Whereas the PKA apoenzyme exists inan open conformation that binds peptide substrate poorly, coordinationof ATP rotates the large and small enzyme lobes, allowing substrate tobind the enzyme in a catalytically active, closed conformation (Akamine,et al., J Mol Biol 2003, 327, 159-71). Our results suggest that 1recognizes the open and closed conformations of PKA with similaraffinities or, alternatively, that the binding of 1 inhibits theconformational changes associated with ATP binding.

The miniature protein conjugate 1-K252a was designed after examinationof the ternary complex of PKA with PKI₅₋₂₄ and the relatedindolocarbazole natural product staurosporine (Prade, et al., Structure1997, 5, 1627-37). This analysis suggested that an octamethylene chainwould appropriately link a C3′ amide derivative of K252a to the sidechain of residue 40 within 1. K252a analogs with conservativesubstitutions at C3′ retain potency against a range of kinases,suggesting that an octamethylene chain at this position would betolerated. Moreover, the PKA-PKI₅₋₂₄ structure shows the side chain ofthe corresponding residue of PKI₅₋₂₄, A21, pointing directly into theATP/staurosporine binding pocket. Accordingly, we synthesizedchloroacetamide K252aΔ (FIG. 5) and a derivative of 1 with a cysteineresidue in place of alanine at position 40 (FIG. 6). 1 ^(A40C) wasalkylated with K252aΔ in the presence of NaI, yielding 1-K252a. K252aΔwas also used to alkylate PKI^(A21C) to produce PKI-K252a.

The inhibitory potencies of 1, 1-1-K252a, PKI-K252a, and K252a itselfwere measured using an assay based on streptavidin-matrix capture ofbiotinylated, [³²P]-phosphorylated substrates in which ATP and peptidesubstrate concentrations were fixed below their respective K_(M) values.As expected, K252a was a potent PKA inhibitor (IC₅₀=0.140±0.003 nM)(FIG. 7 c) and the potency of 1 was similar to its PKA affinity(IC₅₀=117±14 nM) (FIG. 7 d). The miniature protein conjugate 1-K252a was30-fold more potent (IC₅₀=3.65±0.13 nM) than 1 alone (FIG. 7 e).Interestingly, the analogous molecule PKI-K252a was 60-fold less potent(IC₅₀=221±2 nM) than 1-K252a (FIG. 70 and far less potent than PKI(K₁=2.3 nM) (Cheng, et al., J Biol Chem 1986, 261, 989-92). Both 1-K252aand PKI-K252a were far more potent than variants of 1^(A40C) orPKI^(A21C) alkylated with bromoacetamide in place of K252 aΔ (IC₅₀>1 μM,data not shown). The differential potencies of 1-K252a and PKI-K252a mayarise from differences in the affinity of 1 and PKI₅₋₂₄ for the uniqueconformation of PKA observed in ternary complex with PKI₅₋₂₄ andstaurosporine.

To evaluate the extent to which 1 alters the kinase specificity ofK252a, the phosphotransferase assay described above was reconfigured toassay the activities of four distinct but related protein kinases. Aktkinase (PKB), protein kinase Cα (PKC-α) Ca++/calmodulin kinase II(CamKII), and cGMP-dependent protein kinase (PKG) are all inhibited byK252a (FIG. 7 c) but not by PKI₅₋₂₄. Both 1 and 1-K252a showedremarkable specificity for PKA, inhibiting no other kinase tested atconcentrations as high as 100 nM (1-K252a) or 5 μM (1) (FIG. 7 d-e). Theonly other kinase inhibited by 1-K252a was PKG (IC₅₀=679±202 nM), thekinase most similar to PKA (Glass, et al., Biol Chem 1986, 261,12166-71). By contrast, PKI-K252a displayed low specificity, inhibitingall kinases tested with IC₅₀ values within a 4-fold range (FIG. 7 f). Insummary, the PKI₅₋₂₄ conjugate PKI-K252a displayed lower potency thanK252a and lower specificity than PKI₅₋₂₄ whereas the miniature proteinconjugate 1-K252a displayed higher specificity than K252a and higherpotency than 1. Our results suggest that molecules such as 1-K252a thatembody elements of protein surface recognition could represent a viablegeneral strategy for selective kinase inhibition.

Example 19 Miniature Proteins for Activating Transcription ThroughInteractions with The Co-Activator Protein CREB-Binding Protein (CBP):High Affinity Ligands for the CBP KIX Domain

The complex between the KIX domain of the transcriptional coactivatorprotein CBP and the kinase-inducible activation domain (KID) of thetranscription factor CREB, though also mediated by an α-helix, isstrikingly different from the complexes formed by Bcl-2 family members.The KID-binding groove of the CBP KIX domain is quite shallow and moreclosely resembles the solvent-exposed protein surface than a typicalα-helix-binding groove (Radhakrishnan, et al., Cell 1997, 91, 741-752).In fact, only one hydrophobic residue of CREB KID is completely buriedfrom solvent in the KID·KIX complex, and formation of a high affinityKID·KIX complex requires the enthalpic driving force provided byphosphorylation of CREB KID on Ser133 (Mestas, et al., Nat Struct Biol1999, 6, 613-614; Zor, et al., J Biol Chem 2002, 277, 42241-42248).Thus, CBP KIX represents a difficult target for molecular recognition,and indeed, no small molecule ligands for CBP KIX have been reported. Inthis study, protein grafting and molecular evolution by phage displayare used to identify phosphorylated peptide ligands that recognize thehydrophobic surface of CBP KIX with high nanomolar to low micromolaraffinity and high specificity. Furthermore, grafting of the CBPKIX-binding epitope of CREB KID onto the aPP scaffold yields moleculescapable of high affinity and specific recognition of CBP KIX even in theabsence of phosphorylation.

A. Library Design and Generation.

The design of a CBP KIX-binding miniature protein (PPKID) library wasbased on the alignment of the α-helix of aPP and helix B of the CREB KIDdomain shown in FIG. 8B. The otherwise unstructured phosphorylated CREBKID (KID^(P)) domain forms two α-helices, A and B, when bound to the CBPKIX domain; each helix contacts a different region of the CBP KIXsurface (Radhakrishnan, et al., Cell 1997, 91, 741-752). Mutagenesisstudies have determined that most (though not all) of the residues thatcomprise the CBP KIX-binding epitope of CREB KID^(P) are located inhelix B (Radhakrishnan, et al., Cell 1997, 91, 741-752; Parker, et al.,Mol Cell 1998, 2, 353-359), and only residues from helix B were includedin the miniature protein library. Four hydrophobic residues from CREBKID (Tyr134, Ile137, Leu138, Leu141) contribute significantly to thefree energy of KID^(P)·KIX complex formation. The PPKID librarycontained three of these four residues (Ile137, Leu138, Leu141), and aconservative mutation of the fourth from Tyr to Phe, which in thecontext of CREB KID^(P) has no effect on CBP KIX binding (Du, et al.,Mol Cell Biol 2000, 20, 4320-4327). This mutation was included, alongwith the complete recognition site for protein kinase A (PKA; Arg130,Arg131, Ser133), to promote phosphorylation of the miniature proteinlibrary in vitro, if so desired. In the context of CREB KID^(P), the Tyrto Phe mutation lowers five-fold the K_(m) for phosphorylation by PKA(Du, et al., Mol Cell Biol 2000, 20, 4320-4327). The structural scaffoldof the α-helical portion of the library was provided by six of eightresidues (Val14, Leu17, Phe20, Leu24, Tyr27, Leu28) from the aPP α-helixthat contribute to the hydrophobic core (Glover, et al., Biopolymers1983, 22, 293-304). Based on our success using a similar approach toimprove DNA-binding miniature proteins (Chin, et al., J Am Chem Soc2001, 123, 2929-2930), the five residues from the polyproline helix ofaPP known to participate in hydrophobic core formation (Pro2, Gln4,Pro5, Tyr7, Pro8) were varied to all 20 amino acids. Our expectation wasthat the CBP KIX-binding epitope on the α-helix would guide all librarymembers to the CBP KIX surface, and the functional selection wouldidentify those library members with increased CBP KIX affinity derivedfrom packing of the polyproline helix against the otherwise exposed faceof the bound α-helix. A 5×10⁷-member library of miniature proteins(PPKID Library 1) based on this design was generated for use in phagedisplay selection experiments.

B. Selection of Phosphorylated Miniature Protein Ligands for CBP KIX.

Initially, eight rounds of selection were performed (selection 1). Eachround included a PICA-catalyzed in vitro phosphorylation step designedto increase the CBP KIX-binding affinities of all library members.Phosphorylation of CREB KID is critical for high affinity recognition ofCBP KIX; measurements of the contribution of the Ser133 phosphate moietyto the free energy of the KID^(P)·KIX complex range between 1.5 and 3.0kcal·mol⁻¹ (Mestas, et al., Nat Struct Biol 1999, 6, 613-614; Zor, etal., J Biol Chem 2002, 277, 42241-42248). In this selection, GST-KIX wasimmobilized on glutathione-coated microtiter plates, and stringency wasincreased over the course of the selection by increasing the binding andwashing temperature, from 4° C. in round 1 to 25° C. by round 3, and byincreasing the length and number of washes, from 10×1 min washes inround 1 to 20×5 min washes in round 8. Rounds 7 and 8 were performed inbinding buffer containing 5 mM dithiothreitol (DTT), after sequencing ofindividual clones from rounds 4-6 indicated that a significant portionof the library members selected in these rounds contained single Cysresidues. The Cys residues were evenly distributed over all fiverandomized positions, which suggested that library members were beingselected based on their ability to form disulfide bonds with GST-KIX orglutathione, rather than based on high affinity, yet noncovalent, CBPKIX binding.

The progress of the selection was monitored by measuring the retentionof library phage in comparison to the retention of phage displaying aPP,which should not bind to GST-KIX, and by sequencing of individual clonesafter each round of selection. By round 8 of selection 1, the libraryphage were retained 13-fold over aPP phage. Furthermore, by round 7,three sequences (PPKID 1-3) had been identified in multiple independentclones (Table 1); two of these sequences (PPKID2, PPKID3) completelydominated the library by round 8. Surprisingly, the residues selected ateach of the five randomized positions in PPKID2 and PPKID3 displayed nosignificant similarity (PPKID2 and PPKID3 each contain a spuriousmutation not encoded in the original library pool, but the mutation isdifferent in each peptide (Tyr to Asp at position 21 for PPKID2, Leu toArg at position 24 for PPKID3)).

TABLE 1 HisKIX-binding affinity of PPKID and control peptides^(a)Selection 1 K_(d) PPKID^(P) (nM) K_(d) PPKID^(U) (μM) PPKID1GASDMTYWGDDAPVRRLSFFYILLDLYLDAPGVC 591 ± 59 24.1 ± 4.0 PPKID2GMSRVTPGGDDAPVRRLSFFYILRDLYLDAPGVC  729 ± 36 12.6 ± 1.4 PPKID3GASPHTSSGDDAPVRRLSFFDILLDLYLDAPGVC 1200 ± 100  6.7 ± 0.2Selections 2 & 4 K_(d) PPKID^(P) (nM) K_(d) PPKID^(U) (μM) PPKID4GPSQPTYPGDDAPVRRLSFFYILLDLYLDAPGVC  515 ± 44 12.1 ± 2.4 PPKID5GLSWPTYHGDDAPVRRLSFFYILLDLYLDAPGVC  534 ± 31  6.6 ± 2.0 Selections 3 & 4K_(d) PPKID^(P) (nM) K_(d) PPKID^(U) (μM) PPKID6GISWPTFEGDDAPVRRLSFFYILLDLYLDAPGVC 624 ±49  1.5 ± 0.1 PPKID6 S18EGISWPTFEGDDAPVRRLEFFYILLDLYLDAPGVC 10.9 ± 2.0 PPKID7GLSPYTEWGDDAPVRRLSFFYILLDLYLDAPGVC  2.3 ± 0.2 PPKID8GLSWKTDPGDDAPVRRLSFFYILLDLYLDAPGVC  3.1 ± 0.5 Control peptides P: K_(d)U: K_(d) (μM) KID-AB    TDSQKRREILSRRPSYRKILNDLSSDAPGVC 562 ± 41 nM >116KID-B               RRPSYRKILNDLSSDAPGVC 51.6 ± 4.0 uM >297 Peptide C              RRLSFFYILLDLYLDAPGVC  2.4 ± 0.2 uM 21.5 ± 2.6 ^(a)Eachpeptide was labeled on the C-terminal Cys residue withacetamidofluorescein for use in fluorescence polarization experiments.K_(d) values were determined by converting polarization data from threeindependent samples to fraction of fluorescently-labeled peptide boundvalues, which were fit to equilibrium binding equation (2). Residuesselected at randomized positions are in red. Selected point mutations inPPKID2 and PPKID3 are underlined. P indicates a phosphopeptide. Uindicates an unphosphorylated peptide. The phosphoserine residue inphosphopeptides is in bold.

C. CBP KIX-Binding Affinity.

The PPKID peptides were synthesized as phosphopeptides (PPKID^(P)) andeach was labeled with acetamidofluorescein on a C-terminal Cys residue.The affinity of each labeled peptide for a His-tagged CBP KIX domain(HisKIX) was measured by equilibrium fluorescence polarization. TheHisKIX-binding affinities of three phosphorylated control peptides(KID-AB^(P), KID-B^(P) and peptide C^(P)) were also measured. PeptideKID-AB^(P) comprises the full-length CREB KID domain (residues 119-148,A and B helices) and peptide KID-B^(P) corresponds to the region of CREBKID whose residues were incorporated within the α-helix of aPP (residues130-148, the PKA recognition site and helix B); these peptides allowdirect comparison of our miniature proteins with natural CBP KIX-bindingmolecules. Peptide C^(P) corresponds to the chimeric α-helical portionof the PPKID peptides (residues 15-33) and allows us to compare thecontribution to CBP KIX-binding affinity of residues in the α-helixderived from aPP and residues in the randomized region of the PPKIDlibrary, which includes the putative polyproline helix and turn regions.

The results of the equilibrium fluorescence polarization experiments areshown in FIG. 9A and Table 1. KID-AB^(P) binds HisKIX with high affinity(K_(d)=562±41 nM) at 25° C. under the assay conditions used. This valueis lower than previously reported K_(d)s for similar KID^(P)·KIXcomplexes (3.1 μM to 9.7 μM) measured by a number of techniques (thoughnot fluorescence polarization) and may result from slight differences inthe buffers and the CREB KID^(P) and CBP KIX constructs used in eachcase. Peptides PPKID^(P) 1-3 bind HisKIX with affinities ranging from591 nM to 1.2 μM, values that are comparable to the HisKIX-bindingaffinity of KID-AB^(P).

Remarkably, peptides PPKID^(P) 1-3 bind HisKIX with 43- to 87-foldhigher affinity than does KID-B^(P) (K_(d)=51.6±4.0 μM; this value iscomparable to the K_(d) of 80 μM reported for the KID(129-149)^(P)·KIXcomplex measured by isothermal titration calorimetry). Most of thisincrease in affinity can be attributed to the aPP-derived residues inthe α-helical region of the miniature proteins; peptide C^(P) (whichcomprises the α-helical region of PPKID^(P)1-3) binds HisKIX with aK_(d) of 2.4±0.2 μM, which represents a greater than 20-fold increase inaffinity (ΔΔG=−1.8 kcal·mol⁻¹) compared to the CBP KIX-binding affinityof KID-B^(P). The turn and polyproline helix regions (including selectedresidues) of the PPKID^(P)1-3 peptides contribute a more modest-0.4 to−0.8 kcal·mol⁻¹ to the free energy of complex formation with CBP KIX.

The HisKIX-binding affinities of unphosphorylated versions (denoted by asuperscript U) of PPKID 1-3, KID-AB, KID-B and peptide C were alsodetermined (FIG. 9B and Table 1). As expected, the KID-AB^(U) andKID-B^(U) peptides possess very low affinities for HisKIX. Only a smallchange in polarization of the KID-AB^(U)-Flu (61 mP) or KID-B^(U)-Flu(76 mP) molecules was observed even at the highest HisKIX concentrationstested (150 μM and 325 μM, respectively). This experiment allows us toplace a lower limit on the K_(d) of the complex formed between each ofthese peptides and HisKIX. If we estimate the change in polarization ofKID-AB^(U)-Flu to be 110 mP and the change in polarization ofKID-B^(U)-Flu to be 150 mP when fully bound by HisKIX (based on observedchanges in polarization of 116 mP for fully HisKIX-bound KID-AB^(P) and161 mP for KID-B^(P)), we can estimate that the K_(d) of theKID-AB^(U)·HisKIX complex must be greater than 116 μM and the K_(d) ofthe KID-B^(U)·HisKIX complex must be greater than 297 μM. Remarkably,the seven amino acid changes (including the conservative Tyr to Phemutation) that convert KID-B^(U) to peptide C^(U) dramatically enhanceCBP KIX-binding affinity (ΔΔG>−1.5 kcal·mol⁻¹). Peptide C^(U) bindsHisKIX with a K_(d) of 21.5±2.6 μM. Addition of the turn and selectedpolyproline helix regions to yield peptides PPKID^(U)1-3 slightlyincreases or even slightly decreases CBP KIX-binding affinity 1- to3-fold (K_(d)=6.7 to 24.1_(I).LM; MG=−0.7 to +0.1 kcal·mol⁻¹). As istrue in the context of phosphorylated peptides, then, most of the freeenergy of complex formation with HisKIX is due to aPP-derived residuesin the putative α-helical region of the PPKID^(U) peptides.

D. Minimizing Fusion Protein Binding.

Preliminary fluorescence polarization experiments using GST-KIX as atarget indicated that two of the selected peptides (PPKID1 and PPKID3)possessed significantly higher (16- to 19-fold) affinity for GST-KIXthan for HisKIX (data not shown). Therefore, we subjected the members ofPPKID Library 1 to a second selection (selection 2) in which GST-KIX andHisKIX were alternated as the immobilized target protein to minimizeselection of library members based on increased affinity for the GST-KIXor HisKIX fusion proteins relative to the isolated CBP KIX domain.Binding and washing conditions were similar to those used in selection1, and each round included a PKA-catalyzed phosphorylation step. DTT (5mM) was included in the binding buffer in all rounds where GST-KIX wasused as a target (except for round 1) to minimize selection based ondisulfide bond formation. After nine rounds of selection, the libraryphage were retained 44-fold over phage displaying aPP, although noconsensus in miniature protein sequence was achieved. However, twosequences were identified in multiple independent clones from rounds 7-9(PPKID 4-5). Interestingly, PPKID4 contains aPP-derived residues in allrandomized positions. PPKID4 and PPKID5 contain identical residues attwo of the randomized positions, 5 (Pro) and 7 (Tyr), but otherwise theselected residues are not conserved. Furthermore, none of the selectedresidues in either PPKID4 or PPKID5 are similar to the selected residuesin PPKID 1-3. PPKID4 and PPKID5 exhibit high affinity for HisKIX (FIG.9C and Table 1), with K_(d)s in both phosphorylated (515±44 nM and534±31 nM, respectively) and unphosphorylated forms (12.1±2.4 μM and6.6±2.0 μM, respectively) similar to those observed for PPKID 1-3.

E. Unphosphorylated Selections.

The significant CBP KIX-binding affinity displayed by peptide C^(U) (aswell as by short, unphosphorylated CBP KIX-binding peptides identifiedby Montminy and coworkers) encouraged us to perform selections withunphosphorylated PPKID Library 1. Unphosphorylated selections(selections 3 & 4) were performed in parallel with selections 1 & 2,with similar binding and washing conditions. After nine rounds ofselection, the library phage in selection 3 were retained 32-fold overphage displaying aPP, and the library phage in selection 4 were retained11-fold over phage displaying aPP. Although no consensus was reached ineither selection, a number of sequences were identified in multipleindependent clones. In selection 3, one sequence, PPKID6, was identifiedin rounds 6-9. Two of the sequences identified in selection 4, PPKID4and PPKID5, were also identified in selection 2 (which included thephosphorylation step in each round) under the same conditions. Twoadditional sequences, PPKID7 and PPKID8, were identified in rounds 6-9in selection 4.

Interestingly, four of five randomized positions (2, 4, 5, and 7) inpeptides PPKID 4-9 approach consensus; Leu or Ile was selected atposition 2, Trp at position 4, Pro at position 5, and aromatic ornegatively charged residues at position 7. PPKID6^(U), PPKID7^(U) andPPKID8^(U) exhibit exceptionally high affinity for HisKIX, as measuredby fluorescence polarization, with K_(d)s ranging from 1.5 μM to 3.1 μM(FIG. 9C-D and Table 1). These values correspond to at least 37- to77-fold enhancements in HisKIX-binding affinity compared to KID-AB^(U)and at least 96- to 198-fold enhancements relative to KID-B^(U).Furthermore, peptides PPKID^(U) 6-8 bind HisKIX with 7- to 14-foldenhancements in binding affinity compared to peptide C^(U). Thus, theselected polyproline helix and turn regions of the PPKID^(U) 6-8peptides contribute-1.2 to −1.6 kcal·mol⁻¹ to the free energy of complexformation with CBP KIX.

We investigated the HisKIX-binding affinities of two variants of PPKID6,each containing a simple modification of residue Ser18, phosphorylationand substitution of Ser by Glu. Phosphorylation of PPKID6 leads to onlya two-fold enhancement in HisKIX-binding affinity (ΔΔG=−0.5 kcal·mol⁻¹)(FIG. 9D), a significantly smaller enhancement than is observed uponphosphorylation for the other PPKID peptides (6- to 41-fold; ΔΔG=−1.0 to−2.2 kcal·mol¹) and KID-AB (ΔΔG >3.2 kcal·mol⁻¹). Surprisingly, the Serto Glu mutation actually decreases HisKIX-binding affinity 7-fold(K_(d)=10.9±2.0 μM; ΔΔG=+1.2 kcal·mol⁻¹). A similar mutation in thecontext of the full length CREB KID domain leads to CBP KIX-bindingaffinity intermediate between that of unphosphorylated andphosphorylated CREB KID (Shaywitz, et al., Mol Cell Biol 2000, 20,9409-9422) presumably because the negative charge of Glu mimics thenegatively charged phosphate moiety.

F. Binding Modes of PPKID4^(P) and PPKID6^(U).

Two sets of experiments were performed to investigate the binding modesof PPKID4^(P) and PPKID6^(U). First, competition fluorescencepolarization experiments assessed the ability of PPKID4^(P) andPPKID6^(U) to compete with CREB KID^(P) for binding CBP KIX. Inparticular, the fraction of fluorescently tagged PPKID4^(P) orPPKID6^(U) bound to HisKIX at equilibrium was monitored as a function ofthe concentration of unlabeled KID-AB^(P). These experiments reveal thatKID-AB^(P) competes with both PPKID4^(P) and PPKID6^(U) for binding toCBP KIX (FIG. 10). The concentration of KID-AB^(P) needed to displace50% of fluorescently tagged PPKID4^(P) or PPKID6^(U) from HisKIX (theIC₅₀ value) is 3.2 μM or 2.4 μM, respectively. These values are, asexpected given the conditions of the assay (Munson, et al., J Recept Res1988, 8, 533-546), slightly larger than the K_(d) of theKID-AB^(P)·HisKIX complex determined by direct fluorescence polarizationanalysis (562±41 nM). These results indicate that HisKIX cannot interactsimultaneously with KID-AB^(P) and either PPKID4^(P) or PPKID6^(U), andare consistent with an interaction of both PPKID4^(P) and PPKID6^(U)within the CREB KID^(P)-binding cleft of CBP KIX.

Although KID-AB^(P) competes with both PPKID4^(P) and PPKID6^(U) forbinding to HisKIX, small changes in KID-AB^(P) concentration around thecorresponding IC₅₀ values have a larger effect on the change in thefraction of PPKID4^(P) bound than on the change in the fraction ofPPKID6^(U) bound. This result suggests that there may exist differencesin the orientation or geometry of PPKID4^(P) and PPKID6^(U) when boundto CBP KIX. To explore these differences in greater detail, we measuredthe affinities of KID-AB^(P), PPKID4^(P) and PPKID6^(U) for the Y650Avariant of CBP KIX (GST-KIX_(Y650A)) using direct fluorescencepolarization analysis (FIG. 11). Tyr650 forms one side of thehydrophobic cleft within the CREB KID^(P)-binding groove of CBP KIX thataccommodates Leu141 of helix B. As a result, CREB KID^(P) exhibitssignificantly lower affinity for the Y650A variant relative to wild typeCBP KIX. These two factors make GST-KIX_(Y650A) an excellent surveyor ofthe CREB KID^(P)·CBP KIX interface.

The GST-KIX_(Y650A)·KID-AB^(P) complex is 15-fold less stable than thewild type GST-KIX·KID-AB^(P) complex as measured by fluorescencepolarization, a difference in stability similar to that observedpreviously in ITC experiments performed with the same GST-KIXconstructs. Likewise, the PPKID4^(P)·GST-KIX_(Y650A) complex is 24-foldless stable than the wild type GST-KIX·PPKID4^(P) complex. Theobservation that mutation of Tyr650 to Ala has a similar effect on thebinding of KID-AB^(P) and PPKID4^(P), together with the equilibriumcompetition analysis, provides evidence that the two ligands interactwith CBP KIX in a similar manner. Interestingly, despite the fact thatPPKID6^(U) and CREB KID-AB^(P) compete for binding to CBP KIX,PPKID6^(U) binds GST-KIX_(Y650A) with the same affinity (K_(d)=712±68nM) as it binds wild type GST-KIX (K_(d)=714±128 nM). This observationsuggests that PPKID6^(U) interacts with CBP KIX in a manner that issomewhat different from the CBP KIX-binding mode of KID-AB^(P). Furtherwork with an established panel of CBP KIX variants (Parker, et al., MolCell Biol 1999, 19, 5601-5607) currently in progress, will be necessaryto characterize the binding mode of PPKID6^(U) in detail.

G. PPKID Specificity.

Given the myriad protein surfaces present in the cell, the utility ofmolecules that recognize protein surfaces will depend on their abilityto interact selectively with the desired protein. We investigated thespecificity of our highest affinity phosphorylated (PPKID4^(P)) andunphosphorylated (PPKID6^(U)) CBP KIX ligands by measuring theiraffinity for two globular proteins, carbonic anhydrase II andcalmodulin, known to recognize hydrophobic or helical molecules. Todetermine the effect of the region comprising the selected polyprolinehelix and turn on the specificity of PPKID4^(P) and PPKID6^(U), we alsoexamined the specificity of peptide C, in both its phosphorylated andunphosphorylated forms.

The PPKID peptides bind carbonic anhydrase with low affinity, withK_(d)s of 106 ±12 μM and 79±13 μM for PPKID4^(P) and PPKID6^(U),respectively (FIG. 12A and Table 2). These values define specificityratios (K_(rel)=K_(d) (carbonic anhydrase)/K_(d) (HisKIX)) of 205 forPPKID4^(P) and 53 for PPKID6^(U). The preference of PPKID4^(P) forHisKIX over carbonic anhydrase (K_(rel)=205) is considerably higher thanthe preference of control peptide C^(P) for HisKIX over carbonicanhydrase (K_(rel)=40), despite their approximately equal affinity forcarbonic anhydrase (106 μM and 97 μM, respectively). Thus, the increasedspecificity of PPKID4^(P) relative to peptide C^(P) is due to enhancedaffinity for HisKIX, and not a result of decreased affinity for carbonicanhydrase. Similar conclusions are drawn when comparing PPKID6^(U) andpeptide C^(U); although these two molecules display similar affinitiesfor carbonic anhydrase, with K_(d) values of 79 μM and 66 μM,respectively, the specificity ratio for PPKID6^(U) (K_(rel)=53) issignificantly higher than the specificity ratio for peptide C^(U)(K_(rel)=³).

TABLE 2 Specificity of PPKID and control peptides^(a) K_(d) HisKIXK_(d) CA (μM) K_(d) CalM (μM) (μM) (K_(rel)) (K_(rel))PPKID4^(P) GPSQPTYPGDDAPVRRLSFFYILLDLYLDAPGVC 0.515 ± 0.044 106 ± 1252 ± 12 (205) (100) PPKID6^(U) GISWPTFEGDDAPVRRLSFFYILLDLYLDAPGVC 1.5 ±0.1  79 ± 13 >168 (53) (>112)C^(P)                    RRLSFFYILLDLYLDAPGVC 2.4 ± 0.2 97 ± 6 178 ± 42 (40) (74) C^(U)                    RRLSFFYILLDLYLDAPGVC 21.5 ± 2.6  66 ±11 N.D. (3) ^(a)Each peptide was labeled on the C-terminal Cys residuewith acetamidofluorescein for use in fluorescence polarizationexperiments. K_(d) values were determined by converting polarizationdata from two to three independent samples to fraction offluorescently-labeled peptide bound values, which were fit toequilibrium binding equation (2). Residues selected at randomizedpositions are in red. P indicates a phosphopeptide. U indicates anunphosphorylated peptide. The phosphoserine residue in phosphopeptidesis in bold. CA indicates that carbonic anhydrase II was used as thetarget protein; CalM indicates calmodulin was used as the targetprotein. The specificity ratio K_(rel) is defined as K_(rel) = K_(d) (CAor CalM)/K_(d) (HisKIX). N.D. indicates that the value was notdetermined.

The selected PPKID molecules also display a dramatic preference forbinding CBP KIX over calmodulin (FIG. 12B and Table 2). PPKID4^(P) bindscalmodulin with a K_(d) of 51±12 μM, which corresponds to a K_(rel)value of 100. Peptide C^(P) displays slightly lower specificity(K_(rel)=74) than PPKID4^(P) for CBP KIX over calmodulin, a result of5-fold lower affinity for HisKIX and 4-fold lower affinity forcalmodulin (IQ=178±42 μM). The K_(d) for the PPKID6^(U)·calmodulincomplex could not be determined definitively, but we could place a lowerlimit of 168 μM on the K_(d) value by defining the minimum change inpolarization between the fully calmodulin-bound and fully unbound statesof fluorescently labeled PPKID6^(U) as 100 mP (the observed change inthe presence of 185 μM calmodulin was 66 mP). Thus, PPKID6^(U), likePPKID4^(P), exhibits a significant preference for CBP KIX overcalmodulin, with a specificity ratio of at least 112.

In sum, the work described here extends the utility of the proteingrafting and molecular evolution procedure to the significant problem ofhigh affinity and specific recognition of shallow protein surfaces.Taken together with previous applications, the protein grafting strategyhas now proven to be extremely general in scope, enabling the discoveryof highly functional miniature proteins capable of molecular recognitionof diverse nucleic acid and protein targets. In addition, aposttranslational modification step, phosphorylation, was introducedhere for the first time into the molecular evolution protocol used inprotein grafting. Phosphorylated peptide ligands based on the functionalepitope of the CREB KID domain were discovered which possess highnanomolar to low micromolar affinity and high specificity for theshallow surface groove of the CBP KIX domain. Furthermore, presentationof the CREB KID domain functional epitope on the aPP scaffold proteinyielded peptide ligands for CBP KIX which bypass the need forphosphorylation to achieve high affinity CBP KIX recognition and havepotential for use as extremely potent transcriptional activationdomains.

H. Experimental Section.

1) HisKIX expression vector cloning—The CBP KIX-coding region (residues586 to 672) of pGEX-KT KIX 10-672 (a gift from Marc Montminy) (Parker,et al., Mol Cell Biol 1999, 19, 5601-5607) was amplified by PCR using 5′and 3′ primers containing NdeI and BamHI restriction sites,respectively. Primers KIX5P and KIX3P had the following sequences:KIX5P: 5′-GCCGCGCGGCA GCCATATGGG TGTTC GAAAAGCCTGGC-3′; KIX3P:5′-CCAGGCCGCTGCG GATCCTCATCATAA ACGTGACCTCCGC-3′. The CBP KIX-codingduplex DNA insert was digested with NdeI and BamHI and ligated intoNdeI- and BamHI-digested pET15b (Novagen) using T4 DNA ligase (NewEngland Biolabs). The resulting plasmid, pHisKIX, codes for the CBP KIXdomain in-frame with an amino-terminal hexahistidine tag under controlof a T7 promoter. Plasmid identity was confirmed by DNA sequencing ofthe CBP KIX-coding region of pHisKIX.

2) Overexpression and purification of GST-KIX andHisKIX—pGST-ΔKIX(588-683) (a gift from Jennifer Nyborg) (Yan, et al., JMol Biol 1998, 281, 395-400) or pHisKIX was transformed into BL21(DE3)pArg E. coli cells by electroporation. A single colony was used toinoculate a 1 L culture of LB media containing 0.2 mg/mL ampicillin and0.05 mg/mL kanamycin. The culture was incubated at 37° C. with shakingat 250 rpm until the solution reached an optical density of 0.6absorbance units at 600 nm. Isopropyl β-D-thiogalactoside (IPTG) wasadded to a final concentration of 1 mM and incubation continued for 3 hat 37° C. Cells were harvested by centrifugation for 20 min at 10,800 gand resuspended in 15-20 mL of buffer (GST-KIX: 50 mM potassiumphosphate (pH 7.2), 150 mM NaCl, 1 mM DTT; HisKIX: 50 mM sodiumphosphate (pH 8.0), 300 mM NaCl, 10 mM imidazole). Cells were lysed bysonication, insoluble material was pelleted by centrifugation for 30 minat 37,000 g, and the supernatant was retained. GST-KIX and HisKIXproteins were purified by glutathione and nickel-nitrolotriacetic acid(Ni-NTA) affinity chromatography, respectively. Fractions containing thedesired protein were combined, desalted on a NAP 10 (GST-KIX) or NAP 25(HisKIX) column (Amersham) and stored in buffer containing 50 mM Tris(pH 8.0), 100 mM KCl, 12.5 mM MgCl₂, 1 mM ethylenediaminetetraaceticacid (EDTA) and 0.05% Tween-20 (GST-KIX storage buffer also contained 1mM DTT) at −70° C. Protein identity and concentration were confirmed byamino acid analysis.

3) Phage library construction—PPKID Library 1 was created by cassettemutagenesis of the phagemid vector pJC20 (Chin, et al., Bioorg Med ChemLett 2001, 11, 1501-1505) using the synthetic oligonucleotides Align1and PPLib. These oligonucleotides possessed the following sequences (Nindicates an equimolar mixture of G, C, A and T, and S indicates anequimolar mixture of G and C): Align 1: 5′-TGTTCCTT TCTATGCACCGGTTCGTCTCTGTCC TT CTTCTACATCCTGCTGGACCTGTACC TGGACGCACCGGCGGCCGCAGGTGCGCCGGGCC-3′; PPLib: 5′-TGTTCCTTTCTAT GCGGCCCAGCCG GCCGTNNSTCCNNSNNSACCNNSNNSGG TGACGACGCACCG GTAGGTGCGCC GGTGCC-3′. Doublestranded Align1 and PPLib inserts were generated by primer extension ofappropriate primers using Sequenase version 2.0 T7 DNA polymerase (USBiochemicals). The duplex Align1 insert was digested with AgeI and NotI,and purified from a preparative agarose gel using the QIAquick gelextraction kit (Qiagen) and ethanol precipitation. Purified Align1insert was ligated into AgeI- and NotI-digested pJC20 using the LigationExpress Kit (Clontech) to yield the phagemid vector pAlign1. Doublestranded PPLib insert was digested with AgeI and SfiI and purified asper Align1. PPLib insert was ligated into AgeI- and SfiI-digestedpAlign1 using the Ligation Express Kit (Clontech) to generate PPKIDLibrary 1. The ligated PPKID Library 1 phagemid vector was transformedinto XL1 Blue E. coli cells by electroporation and amplified byovernight growth at 37° C. in 2×YT-AG media (2×YT media containing 2%(w/v) glucose and 0.1 mg/mL ampicillin). Glycerol stocks of this culturewere used as the initial pool for selection experiments. PPKID Library 1contained 5×10⁷ independent transformants, which covered the theoreticaldiversity of the library (32⁵=3.36×10⁷) with 77% confidence. Sequencingof twenty individual clones from the initial pool verified the qualityof the library; none of the sequenced clones contained mutations,deletions or insertions in the PPKID-coding region.

4) Phage display procedure—A glycerol stock of the initial pool(round 1) or output from the previous round (rounds 2-9) was used toinoculate 10 mL 2×YT-AG media. The culture was incubated at 37° C. untilit reached an optical density of 0.6 absorbance units at 600 nm. Theculture was then infected with 4×10¹¹ pfu M13K07 helper phage andincubated at 37° C. for 1 h. Cells were pelleted by centrifugation,resuspended in 10 mL 2×YT-AK (2×YT media containing 0.1 mg/mL ampicillinand 0.05 mg/mL kanamycin) and incubated for 12-13 h at 37° C. Cells werethen pelleted by centrifugation and the retained supernatant wasfiltered through a 0.45 μm syringe filter. Phage were precipitated with⅕ volume PEG/NaCl (20% (w/v) PEG-8000, 2.5 M NaCl) on ice for 45 mM, andthen pelleted by centrifugation for 35 min at 24,000 g. Forphosphorylated selections, the precipitated phage were resuspended inwater and approximately 10¹⁰ phage were phosphorylated in vitro with2500 U PKA (Promega) in 100 μM ATP, 40 mM Tris (pH 8), 20 mM magnesiumacetate for 2 h at 30° C. Phosphorylated phage were precipitated on icefor 45 min with PEG/NaCl and then pelleted by centrifugation at maximumspeed in a microcentrifuge for 30 min. Mock phosphorylation reactionswere performed in parallel without PKA, and purified in the same manner.Precipitated phage (+/−PKA treatment) were resuspended in binding bufferfor use in selections. HisKIX binding buffer contained 50 mM potassiumphosphate (pH 7.2), 150 mM NaCl, 0.05% Tween-20 and GST-KIX bindingbuffer contained 20 mM Tris (pH 8.0), 150 mM NaCl, 0.1% Tween-20.

Selections against HisKIX were performed in Ni-NTA HisSorb microtiter8-well strips (Qiagen) and selections against GST-KIX were performed inglutathione-coated 96-well microtiter plates (Pierce). 200 μL targetprotein was added to each well (final concentration of 30 nM for GST-KIXand 100 nM for HisKIX) and incubated overnight with shaking at 4° C.Wells were washed three times with HisKIX or GST-KIX binding buffer toremove unbound protein. For blocking, binding buffer containing 6% milkwas added to each well and incubated at 4° C. for 3 h. After blocking,wells were washed three times with binding buffer. Phage purified asdescribed were added to each well and incubated for 3 h at 4° C. or 25°C. Nonbinding or weakly binding phage were removed by repeated washing(10 to 20 times, 1 min to 5 min in length, according to round) withbinding buffer. Bound phage were eluted by incubation with 0.1 M glycine(pH 2.2) for 20 min. After neutralization of the eluted phage solutionwith 2 M Tris (pH 9.2), XL1 Blue E. coli cells in log phase wereinfected with input and output phage and incubated at 37° C. for 1 h.Serial dilutions of infected cells were plated on SOB agar platescontaining 2% (w/v) glucose and 0.1 mg/mL ampicillin. Cells infectedwith output phage were used to make glycerol stocks and stored at −70°C.

5) Peptide synthesis and modification—Peptides were synthesized on a 25μmol scale at the HHMI Biopolymer/Keck Foundation Biotechnology ResourceLaboratory at the Yale University School of Medicine, New Haven, Conn.All peptides contained free N-terminal amines and amidated C-termini.Phosphoserine residues were introduced using an Fmoc-protectedO-benzyl-phosphoserine derivative with standard coupling conditions.Crude peptides were purified by reverse-phase HPLC on a Vydacsemi-preparative C18 column (300 A, 5 gm, 10 mm×150 mm). Matrix-assistedlaser desorption-ionization time-of-flight (MALDI-TOF) mass spectrometrywas used to confirm peptide identity before further modification.Fluorescein-conjugated derivatives were generated by reaction ofpurified peptides containing single C-terminal cysteine residues with a10-fold molar excess of 5-iodoacetamidofluorescein (Molecular Probes) ina 3:2 mixture of dimethylformamide: phosphate-buffered saline (DMF:PBS).Labeling reactions were incubated with rotation for 3-16 h at roomtemperature. Fluorescein-labeled peptides were purified by reverse-phaseHPLC as described above, and characterized by MALDI-TOF massspectrometry and amino acid analysis.

6) Fluorescence polarization—Fluorescence polarization experiments wereperformed with a Photon Technology International QuantaMaster C-60spectrofluorimeter at 25° C. in a 1 cm pathlength Hellma cuvette. Serialdilutions of HisKIX were made in buffer containing 50 mM Tris (pH 8.0),100 mM KCl, 12.5 mM MgCl₂, 1 mM EDTA, 0.1% Tween-20. Briefly, an aliquotof fluorescently labeled peptide was added to a final concentration of25-50 nM and the binding reaction was incubated for 30 min at 25° C.Thirty minutes was a sufficient length of time for the binding reactionto reach equilibrium, as judged by an absence of change in the observedpolarization value of the sample with the highest HisKIX concentrationover 1 h. For competition experiments, serial dilutions of KID-AB^(P)were incubated with 1.5 μM or 3 μM HisKIX and 25 nM fluorescein-labeledPPKID4^(P) or PPKID6^(U) (peptide^(Flu)) for 60 min at 25° C.,respectively. For specificity measurements, carbonic anhydrase II(Sigma) or calmodulin (Sigma) was used as the target protein in place ofHisKIX, and fluorescently labeled peptide was used at a finalconcentration of 50 nM. Carbonic anhydrase was serially diluted inbinding buffer as described for HisKIX. Calmodulin was serially dilutedin calmodulin folding buffer containing 20 mM Hepes (pH 7.5), 130 mMKCl, 1 mM CaCl₂, 0.05% Tween-20.

Polarization was measured by excitation with vertically polarized lightat a wavelength of 492 nm (10 nm slit width) and subsequent measurementof the fluorescence emission at a wavelength of 515 nm (10 nm slitwidth) for 10 s in the vertical and horizontal directions. Thepolarization data were fit using Kaleidagraph v3.51 software toequilibrium binding equation (1), derived from first principles.

P _(obs) =P _(min)+((P _(max) −P_(min))/(2[peptide^(Flu)]))([peptide^(Flu)]+[target protein]+K_(d)−(([peptide^(Flu)]+[target protein]+K _(d))²−4[peptide^(Flu)][targetprotein])^(0.5))  (1)

In this equation, P_(obs) is the observed polarization at any targetprotein (HisKIX, carbonic anhydrase or calmodulin) concentration,P_(max). is the maximum polarization value, P_(min) is the minimumobserved polarization value, and K_(d) is the equilibrium dissociationconstant. Measurements from two to three independent sets of sampleswere averaged for each dissociation constant determination. For plots offraction of fluorescently labeled peptide (peptide^(Flu)) bound as afunction of target protein concentration, polarization values wereconverted to fraction of peptide^(Flu) bound using the P_(min) andP_(max) values derived from equation (1), and the fraction ofpeptide^(Flu) bound data were fit to equilibrium binding equation (2)using Kaleidagraph v3.51 software.

θ_(obs)=((1/(2[peptide^(Flu)]))([peptide^(Flu)]+[target protein]+K_(d)−(([peptide^(Flu)]+[target protein]+K _(d))²−4[peptide^(Flu)][targetprotein])^(0.5))  (2)

In this equation, θ_(obs) is the observed fraction of peptide^(Flu)bound at any target protein concentration and K_(d) is the equilibriumdissociation constant.

For competition experiments, observed polarization values were convertedto fraction of peptide^(Flu) bound using experimentally determinedP_(min) and P_(max) values corresponding to the polarization of samplescontaining 25 nM peptide alone and peptide^(Flu) with 1.5 μM or 3.0 μMHisKIX, respectively. The fraction of peptide^(Flu) bound data were fitto equation (3) using Kaleidagraph v3.51 software to determine the IC₅₀value.

θ_(obs)=((θ_(max)−θ_(min))/(1([competitor]/IC ₅₀)^(slope)))+θ_(min)  (3)

In this equation, θ_(obs) is the observed fraction of peptide^(Flu)bound at any competitor peptide concentration, slope is defined as theslope at the inflection point and IC₅₀ is the concentration ofcompetitor that reduces binding of peptide^(Flu) by 50%.

Example 20 Characterization of Miniature Proteins as High AffinityLigands for the CBP KIX Domain

A. Do PPKID4^(P) and PPKID6^(U) occupy the CREB KID site on CBP KIX?

In our previous work, we reported that both PPKID4^(P) and PPKID6^(U)bind wild type CBP KIX with high affinity. In the case of PPKID4^(P),the affinity (515±44 nM) was comparable to that of the full lengthphosphorylated CREB KID domain (KID-AB^(P), K_(d)=562±41 nM); PPKID6^(U)bound CBP KIX approximately three-fold worse (K_(d)=1.5 ±0.1 μM) thatdid KID-AB^(P) (Rutledge, et al., J Am Chem Soc 2003, 125, 14336-14347).Here we made use of a set of twelve well-studied CBP KIX variants(Parker, et al., Mol Cell 1998, 2, 353-359) to compare the bindinglocation and orientation of PPKID4^(P) and PPKID6^(U) to that ofKID-AB^(P), whose interactions with CBP KIX have been characterized indetail by NMR (Radhakrishnan, et al., Cell 1997, 91, 741-752). Thesetwelve CBP KIX variants each contain a single alanine substitutionwithin or around the CREB-binding groove, and their affinities forKID-AB^(P) span a 3.7 kcal·mol⁻¹ range (Table 3). We reasoned that ifPPKID4^(P) and PPKID6^(U) interact with CBP in a manner that mimics thatof KID-AB^(P), their affinities for these twelve variants shouldparallel those of KID-AB^(P). The relative affinities of KID-AB^(P),PPKID4^(P) and PPKID6^(U) for the panel of CBP KIX variants weremeasured by equilibrium fluorescence polarization. The results of theseexperiments are shown in FIG. 13 and Table 3.

B. Comparison of the binding modes of PPKID4^(P) and KID-AB^(P).

Recognition of phosphoserine. Recognition of the phosphoserine residuein KID-AB^(P) by CBP KIX contributes heavily to the stability of thecomplex; loss of the phosphate results in a 3.5 kcal·mol⁻¹ loss inbinding free energy. Therefore we first examined whether the PPKID4^(P)phosphoserine contributes significantly to the binding energy of thePPKID4^(P)·CBP KIX complex. The CBP KIX variants Y658F and K662A eachcontain a mutation of a residue that directly contacts the KID-AB^(P)phosphoserine (FIG. 14A). The Y658 side chain donates a phenolichydrogen bond to one terminal phosphoserine oxygen whereas the K662ammonium group forms a salt bridge with a second terminal phosphoserineoxygen. The Y658F and K662A CBP KIX variants both exhibit significantlydecreased affinity for KID-AB^(P), consistent with previous results,with equilibrium dissociation constants of 26±5 and 4.8±0.4 μM,respectively. These values correspond to binding free energies that are2.5 and 1.5 kcal·mol⁻¹ less favorable, respectively, than the wild typeKID-AB^(P)·CBP KIX complex. The free energy changes we measure withthese two variants, as well as the Y658A variant (discussed below), areconsistent with previous work and available structural information.

The Y658F and K662A variants of CBP KIX also exhibit significantlydecreased affinity for PPKID4^(P). The equilibrium dissociation constantof the PPKID4^(P)·Y658F complex is 4.1±0.2 μM. This value corresponds toa binding free energy that is 1.1 kcal·mol⁻¹ less favorable than that ofthe wild type PPKID4^(P)·CBP KIX complex, approximately one half themagnitude of the change seen with KID-AB^(P). The equilibriumdissociation constant of the K662A·PPKID4^(P) complex is 3.9±0.3 μM.This value corresponds to a binding free energy that is 1.1 kcal·mol⁻¹less favorable than that of the wild type PPKID4^(P)·CBP KIX complex,exactly the value measured with KID-AB^(P). These data suggest that theY658 hydrogen bond and the K662 salt bridge each contributesignificantly to the affinity of PPKID4^(P) for CBP KIX. Interestingly,the hydrogen bond to Y658 is more important overall for KID-AB^(P) thanfor PPKID4^(P), whereas the salt bridge with K662 contributes almostequally for both peptides.

We also examined the affinities of KID-AB^(P) and PPKID4^(P) for theY658A variant of CBP KIX in which the entire tyrosine side chain hasbeen replaced by alanine. The NMR structure of the KID-AB^(P)·CBP KIXcomplex shows this aromatic ring packed against residue L128 on helix Aof KID-AB^(P). This variant binds KID-AB^(P) with exceptionally lowaffinity, (K_(d)=142±12 μM) a loss in binding free energy of 3.5kcal·mol⁻¹, presumably because the complex suffers from loss of both thephenolic hydrogen bond and an important hydrophobic packing interaction.Since PPKID4^(P) lacks a residue corresponding to L128 on helix A, onewould expect the stability of the PPKID4^(P)·Y658A complex to becomparable to that of the PPKID4^(P)·Y658F complex. Indeed, theequilibrium dissociation constant of the PPKID4^(P)·Y658A complex is4.1±0.2 μM, corresponding to a free energy loss of 1.1 kcal·mol⁻¹, avalue identical to that measured for the Y658F·PPKID4^(P) complex.

Hydrophobic contacts. Next we considered those residues that line theshallow KID-AB^(P) binding cleft on CBP MX. Six of the twelve variants(L599A, L603A, K660A, Y650A, LL652-3AA and 1657A) contain alanine inplace of a residue within this cleft. For example, Y650 of CBP KIXcomprises one face of the binding cleft and interacts with threehydrophobic side chains of KID-AB^(P), including L138, L141 and A145 onKID-AB^(P) (FIG. 14B). The Y650A variant binds KID-AB^(P) withsignificantly reduced affinity (K_(d)=9.4±0.7 μM), corresponding to a1.8 kcal·mol⁻¹ loss in binding energy. Together, residues L603 and K606form one side of the binding cleft of CBP KIX, interacting with CREBresidues L141 and A145. The L603A and K606A variants bind KID-AB^(P)with equilibrium dissociation constants of 3.4±0.3 and 2.3±0.2 μM,corresponding to losses in binding free energy of 1.2 and 1.0 kcal·mol⁻¹compared to wild type. Other CBP KIX residues that comprise part of thehydrophobic cleft are L653 and 1657; both interact with CREB residueL141 in addition to other residues. As expected, variants LL652-3AA and1657A also bind KID-AB^(P) with lower affinity (K_(d)=2.9±0.2 and1.9±0.1 μM), corresponding to losses in binding free energy of 1.2 and0.9 kcal·mol⁻¹, respectively. Located at the bottom of the bindingcleft, residue L599 interacts with only one residue, P146, of CREB. TheL599A variant binds KID-AB^(P) with lower affinity, but to a lesserextent than other variants that make up the hydrophobic cleft; theKID-AB^(P)·L599A complex has an equilibrium dissociation constant of1.1±0.1 μM, corresponding to a loss in binding free energy of 0.58kcal·mol⁻¹. Thus, as expected, all CBP KIX variants of residues known tomake hydrophobic contacts with CREB bind KID-AB^(P) worse than wild typeCBP KIX.

All six CBP KIX variants within the hydrophobic binding cleft also showdiminished affinity for PPKID4^(P), with equilibrium dissociationconstants between 1.6±0.1 and 3.4±0.5 μM. These K_(d) values correspondto the free energy changes between 0.58 and 1.0 kcal·mol⁻¹. Amazingly,the magnitude and rank order of the affinities of these six CBP KIXvariants for PPKID4^(P) mirror, with only one exception, the affinitiesmeasured for KID-AB^(P). The sole exception to this trend is CBP KIXvariant Y650A; this variant forms a complex with KID-AB^(P) that is 1.8kcal·mol⁻¹ less stable than the wild type complex whereas the complexwith PPKID4^(P) is only 0.95 kcal·mol⁻¹ less stable.

Residues surrounding the binding pocket. In addition to the variantsdescribed above which contain mutations within the KID-AB^(P) bindingpocket, we also examined three variants—E655A, 1660A and Q661A—with analanine substituted at a position surrounding the binding pocket. Thesevariants may provide additional information about the binding site ofligands that do not bind to CBP KIX in the exact same orientation asKID-AB^(P). The equilibrium dissociation constants of the complexes ofthese variants with KID-AB^(P) fall between 0.27±0.03 and 0.93±0.07values very close to that of the wild type complex (ΔΔG=−0.26 and +0.48kcal·mol⁻¹, respectively). These three CBP KIX variants bind PPKID4^(P)with equilibrium dissociation constants between 0.54±0.05 and 1.1±0.1μM, corresponding to free energy changes between-0.07 and 0.35kcal·mol⁻¹; similar to KID-AB^(P), these values are also close to thoseof the wild type complex.

TABLE 3 Equilibrium dissociation constants of complexes betweenPPKID4^(P), PPKID6^(U) and KID-AB^(P) and selected CBP KIX variants. ΔΔGΔΔG ΔΔG K_(d) (μM) (kcal · mol⁻¹) K_(d) (μM) (kcal · mol⁻¹) K_(d) (μM)(kcal · mol⁻¹) CBP KIX KID-AB^(P) PPKID4^(P) PPKID6^(U) wild type 0.41 ±0.04 0.61 ± 0.04 0.54 ± 0.06 Phosphoserine contacts Y658A 142 ± 12  3.53.9 ± 0.3 1.1 1.7 ± 0.4 0.68 Y658F  26 ± 5  2.5 4.1 ± 0.2 1.1 2.8 ± 0.40.97 K662A 4.8 ± 0.4 1.5 3.9 ± 0.3 1.1 1.8 ± 0.3 0.71 Hydrophobiccontacts within cleft Y650A 9.4 ± 0.7 1.8 3.0 ± 0.3 0.95 1.3 ± 0.2 0.52L603A 3.4 ± 0.3 1.2 3.4 ± 0.5 1.0 2.5 ± 0.3 0.91 LL652- 2.9 ± 0.2 1.22.9 ± 0.2 0.93 0.14 ± 0.02 −0.80 3AA K606A 2.3 ± 0.2 1.0 3.1 ± 0.2 0.971.2 ± 0.1 0.47 I657A 1.9 ± 0.1 0.90 2.7 ± 0.1 0.89 3.6 ± 0.4 1.1 L599A1.1 ± 0.1 0.58 1.6 ± 0.1 0.58 3.3 ± 0.3 1.1 Hydrophobic contacts outsidecleft Q661A 0.93 ± 0.07 0.48 1.1 ± 0.1 0.35 0.41 ± 0.06 −0.16 E655A 0.71± 0.05 0.32 0.54 ± 0.05 −0.07 1.7 ± 0.2 0.68 I660A 0.27 ± 0.03 −0.26 1.1± 0.1 0.35 6.1 ± 0.7 1.4C. Comparison of the binding modes of PPKID6^(U) and KID-AB^(P).

Recognition of phosphoserine. PPKID6^(U) lacks the phosphoserine thatdominates the energetics of the PPKID4^(P)·CBP KIX and KID-AB^(P)·CBPKIX complexes. Therefore, if this ligand is bound in a manner thatmirrors that of PPKID4^(P) and KID-AB^(P), it should be less sensitiveto changes at positions Y658 and K662 of CBP KIX. Surprisingly,PPKID6^(U) binds both variants with significantly decreased affinityrelative to wild type CBP KIX. The equilibrium dissociation constants ofthe Y658F·PPKID6^(U) and K662A·PPKID6^(U) complexes are 2.8±0.4 and1.8±0.3 μM, corresponding to free energy losses of 0.97 and 0.71kcal·mol⁻¹, respectively, relative to the wild type complex.Interestingly, the Y658A variant binds PPKID6^(U) better (K_(d)=1.7±0.4μM) than the Y658F variant (K_(d)=2.8±0.4 μM), whereas Y658A and Y658Fbind PPKID4^(P) equally well. These results are not consistent with amodel in which the α-helix in PPKID6^(U) is positioned within the CBPKIX cleft in a manner that closely mimics that of KID-AB^(P). Incontrast, they support a model characterized by an overlapping, butalternate, binding mode for PPKID6^(U) compared to PPKID4^(P) andKID-AB^(P).

Hydrophobic contacts. Mutation of the KIX side chains that line theKID-AB^(P) binding pocket in CBP KIX (variants L599A, L603A, K606A,Y650A and 1657A) results in complexes with PPKID6^(U) that are 0.47 to1.1 kcal·mol⁻¹ less stable than the wild type complex. In contrast, thecomplex with LL652-3AA is 0.8 kcal·mol⁻¹ more stable. Variants L599A,L603A, and 1657A exhibit moderately diminished binding affinity toPPKID6^(U) (K_(d)=3.3±0.3, 2.5±0.3, and 3.6±0.4 μM; & ΔΔG=1.1, 0.91, and1.1 kcal·mol⁻¹, respectively), whereas K606A and Y650A show smallerdecreases in PPKID6^(U) binding affinity (K_(d)=1.2±0.1 and 1.3±0.2 μM;MG=0.47 and 0.52 kcal·mol⁻¹, respectively). Ranking of the hydrophobiccontact residues in order of energetic contribution to complex formationwith each ligand reveals a pattern for PPKID6^(U) binding unlike thatfor KID-AB^(P) or PPKID4^(P). For example, Y650 and L599 make thelargest and smallest energetic contributions, respectively, to bindingof KID-AB^(P), whereas Y650 contributes least and L599 contributes mostto complex formation with PPKID6^(U).

Residues surrounding the binding pocket. Although CBP KIX variantsE655A, 1660A and Q661A display affinities for KID-AB^(P) and PPKID4^(P)comparable to wild type CBP KIX, two of these variants showsignificantly diminished affinity for PPKID6^(U). Variant 1660A exhibitsthe largest decrease in PPKID6^(U) binding affinity of all CBP KIXvariants in the panel, with an equilibrium dissociation constant of6.1±0.7 μM, corresponding to a free energy loss of 1.4 kcal·mol⁻¹. E655Aalso exhibits decreased affinity for PPKID6^(U), albeit to a lesserextent (K_(d)=1.7±0.2 μM; ΔΔG=0.68 kcal·mol⁻¹), whereas Q661A bindsPPKID6^(U) with affinity comparable to wild type CBP KIX. Again,differences in the relative and absolute contributions of CBP KIXresidues to the energy of complex formation with PPKID6^(U) compared toPPKID4^(P) and KID-AB^(P) suggest an alternate, but overlapping bindingsite for PPKID6^(U).

D. Is PPKID4^(P) Folded when Bound to CBP KIX?

The results described above suggest that the α-helix in PPKID4^(P) ispositioned within the CBP KIX cleft in a manner that closely mimics thatof KID-AB^(P), but shed no light on whether PPKID4^(P) is folded into anaPP-like hairpin conformation when bound. We previously reported thatPPKID4^(P) displays only nascent α-helicity in water in the absence ofCBP KIX, as determined by circular dichroism. To explore whetherPPKID4^(P) folds into an aPP-like hairpin conformation upon binding toCBP MX, we prepared a set of eleven PPKID4^(P) variants in which alanineor sarcosine is substituted for a PPKID4^(P) residue that comprises thehydrophobic core in the putative folded state (Blundell, et al., ProcNatl Acad Sci USA 1981, 78, 4175-4179). These variants include alaninesubstitutions along the face of the PPKID4^(P) α-helix opposite the faceused to contact CBP KIX (L17A, F20A, L24A, L28A and Y27A) and sixvariants with alanine or sarcosine substitutions along the PPII helix(P2A, P2Z, P5A, P5Z, P8A and P8Z). A close-up view of packing in thehydrophobic core is shown in FIG. 15.

We hypothesized that if PPKID4^(P) folds upon binding within the CBP KIXbinding cleft into an aPP-like conformation, then the stability of itscomplex with CBP MX would depend on the presence of residues thatcomprise the intact hydrophobic core in a manner commensurate with theircontribution to core stability, and the corresponding variants woulddisplay diminished affinity for CBP KIX. However, if the N-terminalregion of PPKID4^(P) interacts with the CBP KIX surface elsewhere, thenthe stability of the PPKID4^(P)·CBP KIX complex would not depend on theidentities of putative folding residues from the PPKID4^(P) α-helix. Inthis case, the variants would display affinity for CBP KIX comparable towild type PPKID4^(P).

TABLE 4 Binding affinities of PPKID4^(P) variants for CBP KIX asdetermined by fluorescence polarization. ΔΔG PPKID4^(P) K_(d) (μM) (kcal· mol⁻¹) Wild type 0.61 ± 0.04 Polyproline helix variants P2A 0.87 ±0.04 0.21 P2Z 0.83 ± 0.08 0.18 P5A 1.02 ± 0.09 0.30 P5Z 0.80 ± 0.03 0.16P8A 1.07 ± 0.08 0.33 P8Z 0.78 ± 0.05 0.15 α-helix variants L17A 0.68 ±0.05 0.07 F20A 2.55 ± 0.25 0.85 L24A 1.16 ± 0.07 0.38 Y27A 3.09 ± 0.180.96 L28A 0.83 ± 0.11 0.18

E. Effects of PPKID4^(P) Variants on CBP KIX Binding.

We used fluorescence polarization analysis to determine the CBP KIXbinding affinities of eight PPKID4^(P) variants in which one residuewithin the aPP hydrophobic core had been substituted with alanine. Fiveof these residues lie on the internal face of the aPP □helix, whereasthree lie on the internal face of the PPII helix. We also studied threevariants in which a proline residue on the internal face of the PPIIhelix was substituted by sarcosine (FIG. 16 and Table 4). Theequilibrium dissociation constants of the PPKID4^(P) variant·CBP KIXcomplexes range from 0.68±0.05 to 3.09±0.18 μM, corresponding to bindingenergies between 0.07 and 0.96 kcal·mol⁻¹ less favorable than the wildtype complex. The stabilities of the variant complexes fall naturallyinto three categories. The least stable complexes containing variantsF20A and Y27A were 0.85 and 0.96 kcal·mol⁻¹ less stable than the wildtype complex; moderately stable complexes containing variants P5A, P8Aand L24A were 0.3 to 0.38 kcal·mol⁻¹ less stable than the wild typecomplex. Six of the variants, P2A, P2Z, P5Z, P5Z, L 17A and L28A, formedCBP KIX complexes with stabilities that were similar (0.07 to 0.21kcal·mol⁻¹) to the wild type complex. It is striking that that thoseside chains that contribute significantly or moderately to the stabilityof the PPKID4^(P)·CBP KIX complex—F20, L24, Y27, P5 and P8—all lie atthe center of the aPP hydrophobic core (FIG. 15). The aromatic sidechain of F20 inserts between the side chains of residues P3 and P5, thebranched side chain of L24 packs against P8 and F20, and the side chainof Y27 packs against P8. By contrast, those side chains that contributeminimally to stability—P2, L17 and L28—lie at the edge of thehydrophobic core of aPP and participate in fewer van der Waalsinteractions. Thus, these results support a model in which PPKID4^(P)folds (although to a lesser extent than aPP) upon binding to CBP KIXinto an aPP-like hairpin conformation.

F. Can PPKID Peptides Function as Transcriptional Activation Domains inCultured Cells?

Eukaryotic transcriptional activators, such as CREB, stimulate geneexpression primarily by recruitment of the general transcriptionmachinery to the promoters of the genes they regulate (Ptashne, et al.,Genes & Signals; Cold Spring Harbor Laboratory: New York, 2002). Thesetranscription factors are modular in nature, containing a DNA bindingdomain that targets the activators specifically to the gene of interest,and an activation domain that binds, and thereby recruits, thetranscriptional machinery. The functions of these two domains areseparable; domains can be swapped among different activator proteins, orindeed replaced altogether with non-natural counterparts, to obtainmolecules with novel activation activities (Ansari, et al., Curr OpinChem Biol 2002, 6, 765-772). The development of fully artificialactivators is an important goal in chemical biology, but although therehas been considerable success in the development of novel DNA bindingmolecules, the development of artificial activation domains lags behind(Mapp, Organic and Biomolecular Chemistry 2003, 1, 2217-2220). By virtueof their ability to bind CBP, a coactivator protein that bridgestranscription factors and the basal transcription machinery, wehypothesized that PPKID4^(P) and PPKID6^(U) might function as artificialactivation domains when fused to a heterologous DNA-binding domain.

To investigate the activation potential of these ligands, we prepared aseries of mammalian expression plasmids containing the CBP KIX ligandsKID-AB, PPKID4 or PPKID6 fused to the C-terminus of the Gal4 DNA-bindingdomain (DBD) (residues 1-147). As a control, we used pAL1, whichcontained the Ga14 DBD alone. These constructs were transfected intoHEK293 cells along with a previously described reporter plasmidcontaining five Ga14 binding sites upstream of the firefly luciferasegene (FIG. 17A) and a plasmid encoding Renilla luciferase to control forvariable transfection efficiency. The cells were incubated at 37° C. for36 h, lysed, and the ratio ® of activity of firefly and Rinellaluciferase measured using the Dual-Luciferase® Reporter Assay System(Promega). The potency of each activation domain (fold activation) wasdetermined by dividing the values measured in cells transfected with aGa4 DBD fusion by the value measured in cells transfected with the pAL1control. Based on a previous study that found a correlation between theCBP KIX-binding affinity and activation potency of short peptides(Frangioni, et al., Nat Biotechnol 2000, 18, 1080-1085), we expectedPPKID4^(P) and PPKID6^(U) to activate transcription at level comparableto KID-AB^(P) due to their similar affinities for CBP KIX.

G. Activation Potential of PPKID4, PPKID6 and KID-AB.

First, we investigated the ability of KID-AB, PPKID4, and PPKID6 toactivate transcription in the absence of forskolin, wherephosphorylation of cellular proteins is not stimulated (FIG. 17B). Wepreviously reported that PPKID4 and KID-AB possess low affinity for CBPKIX under these conditions (Rutledge, et al., J Am Chem Soc 2003, 125,14336-14347) and would not be expected to effectively recruit CBP to theGa14 promoter. Indeed, Ga14 DBD fusion proteins containing PPKID4 orKID-AB did not stimulate transcription over basal levels under theseconditions. The fold increase in transcription measured in cellstransfected with plasmids encoding these two fusion proteins was nohigher than in cells transfected with PPKID6 also failed to activatetranscription under these conditions, despite possessing significantaffinity (Kd=1.5 μM) for CBP KIX.

Next, we investigated the ability of KID-AB, PPKID4 and PPKID6 toactivate transcription under conditions where phosphorylation isstimulated. Addition of forskolin to the cell culture media induces thecAMP pathway, which activates protein kinase A (PKA) and leads to thephosphorylation of PKA substrates, including KID-AB and the PPKIDpeptides (Gonzalez, et al., Cell 1989, 59, 675-680; Johannessen, et al.,Cell Signal 2004, 16, 1187-1199). As phosphorylation of KID-AB andPPKID4 dramatically increases their CBP KIX-binding affinity, weexpected that phosphorylation of these ligands will also increase theirability to recruit CBP and hence, their transcriptional potency. Indeed,in the presence of forskolin, KID-AB and PPKID4 activate transcription7.5-fold over basal levels. Phosphorylation of PPKID6 also increases itsCBP KIX-binding affinity; however, with only 2-fold higher affinity forCBP KIX, it was not clear whether PPKID6^(P) would be capable ofactivating transcription when PPKID6^(U) could not. In fact, in thepresence of forskolin, PPKID6 activated transcription 2.5-fold overbasal levels.

H. Does Transcriptional Activation by the PPKID Peptides Occur Via theCBP/p300 Pathway?

Transcriptional activation by CREB KID occurs via recruitment of CBP topromoters where CREB is bound. However, transcription can be activatedby a variety of different pathways. Therefore, it was of great interestto investigate whether, as we hypothesize, the observed transcriptionactivation potential of PPKID4^(P) and PPKID6^(P) is dependent onrecruitment of CBP. Towards this end, we compared the transcriptionpotential of PPKID4^(P) and PPKID6^(P) in the presence and absence ofexogenous p300, a paralog of CBP. An increase in the effectiveconcentration of p300 in the cells should lead to an increase intranscriptional activation that occurs via the p300/CBP pathway. Thus,we expected that the levels of transcription activation elicited byPPKID4^(P) and PPKID6^(P) in the presence of exogenous p300 would besignificantly higher than the levels of transcription observed with onlyendogenous CBP/p300.

As expected, in the presence of additional p300, KID-AB^(P) activatedtranscription 20-fold over basal levels, confirming that theconcentration of endogenous CBP/p300 in HEK293 cells is limiting (FIG.17C). Similarly, PPKID4^(P) activated transcription 20-fold over basallevels in the presence of exogenous p300, a 2.7-fold increase relativeto PPKID4^(P)-dependent transcription mediated by endogenous CBP/p300alone. Likewise, PPKID6^(P) activated transcription 15-fold over basallevels in the presence of additional p300, a 6-fold increase relative toPPKID6^(P)-dependent transcription mediated by endogenous CBP/p300.Somewhat surprisingly, addition of p300 also increased transcriptionactivation by PPKID6 in the absence of phosphorylation to levels4.5-fold over basal transcription levels, whereas PPKID6 failed toactivate transcription in the presence of only endogeous CBP/p300. Thus,although unphosphorylated PPKID6 is perhaps best described as a weakactivation domain, it nevertheless activates transcription via theCBP/p300 pathway. These results are consistent with a model in whichPPKID4 and PPKID6, like CREB KID, activate transcription by recruitmentof CBP/p300 via the KIX domain to the promoters where they are bound.

I. Transcription Inhibition by PPKID4^(P).

We have shown that transcriptional activation by PPKID4^(P) andPPKID6^(P) occur via the same pathway as CREB KID, the CBP/p300 pathway.Therefore it would be of interest to show that these activation domainsindeed compete with each other to activate transcription in livingcells. We compared the transcription potential of PPKID6^(P), PPKID4^(P)and KID-AB^(P) in the presence of increasing amounts of the PPKID4^(P)activation domain (without a DNA-binding domain). It is expected thatincreasing amounts of the PPKID4^(P) activation domain will bind thelimited supply of CBP in the cells, thus preventing transcription viathe CBP/p300 pathway. Based on the above results, we hypothesize thatthe PPKID4^(P) activation domain will inhibit transcription of thephosphorylated PPKID and CREB ligands.

As expected, transcriptional activation by PPKID4^(P) was significantlyreduced when a 2:1 ratio of PPKID4^(P) activation domain:Ga14DBD-PPKID4^(P) was transfected in HEK293 cells. Cotransfection of a5-fold excess of PPKID4^(P) activation domain brought activation down tobasal levels. Activation by KID-AB^(P) was inhibited when a 5:1 ratio ofPPKID4^(P) activation domain:Gal4 DBD-KID-AB^(P) was transfected. With a10-fold excess of the PPKID4^(P) activation domain, KID-AB^(P)activation was completely inhibited. Due to its low level of activation,PPKID6^(P) activation is brought down to basal levels in the presence ofonly a 2-fold excess of the PPKID4^(P) activation domain.

In sum, the binding mode and orientation of two ligands for CBP KIX(PPKID4^(P) and PPKID6^(U)) designed to mimic the natural ligandKID-AB^(P) have been investigated. Binding affinity data with CBP KIXvariants show that (despite conformational differences) PPKID4^(P) bindsin the same hydrophobic pocket of CBP KIX as KID-AB^(P), possiblydirected to this site by the phosphate group. Our results support amodel in which PPKID4^(P) folds into an aPP-like conformation uponbinding to CBP MX. PPKID6^(U) binds an overlapping yet distinct regionof CBP MX. The distance separating the CBP KIX residues critical forbinding this ligand suggests that PPKID6^(U) binds in an openconformation. These ligands do not only bind their target with highaffinity in vitro, but they also function in mammalian cells. PPKID4^(P)and PPKID6^(P) function as transcriptional activators much like thetranscription factor CREB after which they were modeled. These ligandscan act as artificial activation domains, and have the potential toserve as tools in understanding the mechanism of transcriptionactivation.

J. Experimental Section.

1) Expression and purification of CBP KIX and KIX mutants—See above inExample 19.

2) Peptide Synthesis and Modification—PPKID4^(P), PPKID6^(U) andKID-AB^(P) peptides were synthesized as described above in Example 19.

3) Fluorescence Polarization—See above in Example 19.

4) Gal4 DBD-peptide constructs—Peptides were cloned into a BamHI andSalI digested pAl₁ vector (a gift from John Frangioni) (Voss, et al.,Anal Biochem 2002, 308, 364-372), which encodes the Gal4 DNA-bindingdomain and results in fusion of the peptide to the C-terminus to theGal4 DBD. For PPKID4 inhibition experiments, PPKID4 was cloned into aBglII and BamHI digested pAl_(l) vector, which removes the Gal4 DBD.

5) Cell Culture, Transfection and Luciferase Assays—HEK293 cells(CRL-1573 ATCC) were grown in DMEM containing 10% fetal bovine serum.Cells were plated in 24-well plates 24 hours prior to transfection.Cells were transfected using SuperFect transfection reagent (Qiagen)with 800 ng of total DNA. Included were 5 ng of peptide-Gal4 DNA-bindingdomain construct, 400 ng of 5× Gal4 firefly luciferase reporter plasmid(a gift from John Frangioni), 20 ng of a promoterless Renilla luciferaseplasmid (Promega) for normalization and pBluescript SK+ carrier DNA.Where indicated forskolin was added to cell media 6 hours beforeharvested. Cells were harvested and assayed 36 hours after transfectionand Turner Designs Model TD-20/20 luminometer.

Example 21 Preparation of a Universal Miniature Protein Phage DisplayLibrary

A combinatorial library designed to be used generally in the discoveryand engineering of miniature proteins can also be constructed using themethods of the invention. This universal library is designed to displaya combinatorial set of epitopes to enable the recognition of nucleicacids, proteins or small molecules by a miniature protein without priorknowledge of the natural epitope used for recognition. The universallibrary optimally is formed by varying (at least about) six residues onthe solvent-exposed face of aPP which do not contribute to the formationof the hydrophobic aPP core. These residues of aPP include Tyr21, Asn22,Asp22, Gln23 and Asn26. All members of this universal library willretain the remarkable stability and compact structure of avianpancreatic polypeptide while introducing a diverse, functional,solvent-exposed surface available for recognition. The number ofindependent transformants (2.5×10⁹ clones) required to cover sequencespace of a six-membered library is experimentally feasible.

INCORPORATION BY REFERENCE

All publications and patents mentioned herein are hereby incorporated byreference in their entirety as if each individual publication or patentwas specifically and individually indicated to be incorporated byreference.

While specific embodiments of the subject invention have been discussed,the above specification is illustrative and not restrictive. Manyvariations of the invention will become apparent to those skilled in theart upon review of this specification and the claims below. The fullscope of the invention should be determined by reference to the claims,along with their full scope of equivalents, and the specification, alongwith such variations.

1. A modified avian pancreatic polypeptide (aPP) comprising substitution of at least one amino acid residue, said at least one residue being exposed on the alpha helix domain of the polypeptide when the polypeptide is in a tertiary form, wherein the modified polypeptide binds to a target protein.
 2. The modified polypeptide of claim 1, wherein at least six residues are substituted. 3-5. (canceled)
 6. The modified polypeptide of claim 1, wherein the site is a protein-binding site.
 7. The modified polypeptide of claim 1, wherein said at least one substituted residues are from any site of a known protein through which the known protein interacts with its binding partner.
 8. The modified polypeptide of claim 7, wherein the target protein is a binding partner of the known protein.
 9. The modified polypeptide of claim 7, wherein the known protein is selected from the group consisting of a Bcl2 protein, p53, a protein kinase inhibitor (PKI), and CREB.
 10. The modified polypeptide of claim 7, wherein the binding partner is selected from the group consisting of a Bcl2 protein, MDM2, protein kinase A, and CBP.
 11. The modified polypeptide of claim 7, wherein the modified polypeptide inhibits interaction between the known protein and the binding partner.
 12. The modified polypeptide of claim 7, wherein the modified polypeptide binds to a deep groove of the target protein.
 13. The modified polypeptide of claim 12, wherein the groove is more than 6 Å at deepest point.
 14. The modified polypeptide of claim 7, wherein the modified polypeptide binds to a shallow groove of the target protein.
 15. The modified polypeptide of claim 14, wherein the groove is less than 6 Å at deepest point.
 16. The modified polypeptide of claim 1, wherein the modified polypeptide binds to the target protein with a Kd of less than 1 micromolar.
 17. The modified polypeptide of claim 1, wherein the modified polypeptide binds to the target protein with high specificity.
 18. (canceled)
 19. A stabilized miniature protein comprising a miniature protein and a second portion comprising a stabilizing domain, wherein the miniature protein is a modified avian pancreatic polypeptide (aPP) comprising substitution of at least one amino acid residue, said at least one residue being exposed on the alpha helix domain of the polypeptide when the polypeptide is in a tertiary form, wherein the modified polypeptide binds to a target protein.
 20. The stabilized miniature protein of claim 19, wherein the second portion is a polypeptide covalently fused to the miniature protein.
 21. The stabilized miniature protein of claim 20, wherein the second portion is selected from the group consisting of serum albumin and an IgG Fc domain.
 22. The stabilized miniature protein of claim 19, wherein the second portion is a non-amino acid moiety.
 23. The stabilized miniature protein of claim 19, wherein said miniature protein includes one or more modified amino acid residues selected from the group consisting of a phosphorylated amino acid, a glycosylated amino acid, a PEGylated amino acid, a farnesylated amino acid, an acetylated amino acid, a biotinylated amino acid, an amino acid conjugated to a lipid moiety, and an amino acid conjugated to an organic derivatizing agent. 24-38. (canceled)
 39. A method of preparing a miniature protein that modulates the interaction between a known protein and another molecule, comprising the steps of: (a) identifying at least one amino acid residue that contributes to the binding between a known protein and another molecule; and (b) modifying an avian pancreatic polypeptide by substitution of said at least one amino acid residue, such that it is exposed on the alpha helix domain of the polypeptide when the polypeptide is in a tertiary form. 40-63. (canceled) 